Starting phenix.real_space_refine on Thu Sep 18 03:38:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9boy_44754/09_2025/9boy_44754.cif Found real_map, /net/cci-nas-00/data/ceres_data/9boy_44754/09_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_44754/09_2025/9boy_44754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9boy_44754/09_2025/9boy_44754.map" model { file = "/net/cci-nas-00/data/ceres_data/9boy_44754/09_2025/9boy_44754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9boy_44754/09_2025/9boy_44754.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 1, '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: {'ARG:plan': 4, 'GLU:plan': 1, '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: {'ARG:plan': 3, 'GLU:plan': 2, '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: {'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} 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: 4.37, per 1000 atoms: 0.32 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: 1.23 Conformation dependent library (CDL) restraints added in 757.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.55 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: 2.61 Time building geometry restraints manager: 1.63 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: 1.540 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.340 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- 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 : 11.74 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG C 27 TYR 0.020 0.001 TYR B 301 PHE 0.019 0.001 PHE C 306 TRP 0.062 0.002 TRP A 239 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00382 (14170) covalent geometry : angle 0.62467 (19267) SS BOND : bond 0.00285 ( 10) SS BOND : angle 1.70022 ( 20) hydrogen bonds : bond 0.17909 ( 638) hydrogen bonds : angle 8.00558 ( 2046) link_NAG-ASN : bond 0.00906 ( 5) link_NAG-ASN : angle 2.57657 ( 15) *********************** 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 : 0.572 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: 0.1043 time to fit residues: 36.3077 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 : 0.646 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 186 GLN E 173 GLN E 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101093 restraints weight = 38051.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103327 restraints weight = 20446.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103971 restraints weight = 16415.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104523 restraints weight = 11940.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106495 restraints weight = 10478.045| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0908 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= 0.123 Angle : 0.603 7.848 19302 Z= 0.307 Chirality : 0.045 0.200 2195 Planarity : 0.004 0.031 2411 Dihedral : 6.262 58.442 2001 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 2.27 % Allowed : 14.40 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.21), residues: 1695 helix: 1.83 (0.22), residues: 548 sheet: -1.00 (0.29), residues: 351 loop : -0.85 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 27 TYR 0.022 0.001 TYR B 301 PHE 0.015 0.001 PHE B 48 TRP 0.049 0.001 TRP A 239 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00260 (14170) covalent geometry : angle 0.59691 (19267) SS BOND : bond 0.00430 ( 10) SS BOND : angle 1.43703 ( 20) hydrogen bonds : bond 0.04218 ( 638) hydrogen bonds : angle 5.43904 ( 2046) link_NAG-ASN : bond 0.00631 ( 5) link_NAG-ASN : angle 2.66180 ( 15) *********************** 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 254 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8293 (p0) cc_final: 0.7857 (p0) REVERT: A 266 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8618 (tt0) REVERT: A 287 MET cc_start: 0.8058 (tpp) cc_final: 0.7558 (mmm) REVERT: B 56 MET cc_start: 0.8131 (tpp) cc_final: 0.7915 (mtp) REVERT: B 103 GLU cc_start: 0.8528 (tt0) cc_final: 0.8307 (tt0) REVERT: B 188 LEU cc_start: 0.8965 (tp) cc_final: 0.8557 (pp) REVERT: B 252 ARG cc_start: 0.8488 (mtp180) cc_final: 0.8146 (mmm-85) REVERT: B 263 MET cc_start: 0.8374 (mmm) cc_final: 0.8068 (mmm) REVERT: B 391 ARG cc_start: 0.6897 (mpp80) cc_final: 0.6228 (mmm160) REVERT: C 225 ILE cc_start: 0.9178 (tp) cc_final: 0.8936 (tp) REVERT: D 102 ASN cc_start: 0.8525 (p0) cc_final: 0.7745 (p0) REVERT: D 147 MET cc_start: 0.8136 (mpp) cc_final: 0.7712 (mtp) REVERT: D 226 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 292 LEU cc_start: 0.8969 (mm) cc_final: 0.8542 (tp) REVERT: E 125 ASN cc_start: 0.8637 (t0) cc_final: 0.8044 (t0) REVERT: E 126 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8849 (tm-30) REVERT: E 133 ASP cc_start: 0.7703 (p0) cc_final: 0.7229 (p0) REVERT: E 135 THR cc_start: 0.8674 (p) cc_final: 0.8459 (t) REVERT: E 217 GLU cc_start: 0.7658 (pm20) cc_final: 0.7445 (pm20) REVERT: E 243 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6904 (mt0) outliers start: 34 outliers final: 24 residues processed: 238 average time/residue: 0.1023 time to fit residues: 38.0245 Evaluate side-chains 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 55 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 0.0170 chunk 46 optimal weight: 0.8980 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.132333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102194 restraints weight = 42451.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104334 restraints weight = 22628.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104535 restraints weight = 20150.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106822 restraints weight = 12428.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107144 restraints weight = 9403.417| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1105 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= 0.123 Angle : 0.580 9.447 19302 Z= 0.293 Chirality : 0.044 0.197 2195 Planarity : 0.003 0.032 2411 Dihedral : 5.551 57.440 1975 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.19 % Favored : 96.69 % Rotamer: Outliers : 2.60 % Allowed : 16.13 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.21), residues: 1695 helix: 1.75 (0.22), residues: 554 sheet: -0.94 (0.29), residues: 352 loop : -0.84 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.021 0.001 TYR B 301 PHE 0.016 0.001 PHE B 410 TRP 0.041 0.001 TRP A 239 HIS 0.002 0.000 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00270 (14170) covalent geometry : angle 0.57452 (19267) SS BOND : bond 0.00370 ( 10) SS BOND : angle 1.18870 ( 20) hydrogen bonds : bond 0.03902 ( 638) hydrogen bonds : angle 5.05339 ( 2046) link_NAG-ASN : bond 0.00476 ( 5) link_NAG-ASN : angle 2.57345 ( 15) *********************** 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: 39 poor density : 216 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8340 (p0) cc_final: 0.7894 (p0) REVERT: A 226 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 261 LEU cc_start: 0.8990 (tp) cc_final: 0.8528 (pp) REVERT: A 287 MET cc_start: 0.7964 (tpp) cc_final: 0.7478 (mmm) REVERT: B 103 GLU cc_start: 0.8569 (tt0) cc_final: 0.8327 (tt0) REVERT: B 188 LEU cc_start: 0.8982 (tp) cc_final: 0.8555 (pp) REVERT: B 391 ARG cc_start: 0.6996 (mpp80) cc_final: 0.6303 (mmm160) REVERT: C 225 ILE cc_start: 0.9148 (tp) cc_final: 0.8855 (tp) REVERT: C 287 MET cc_start: 0.7969 (mmm) cc_final: 0.7454 (mmm) REVERT: D 102 ASN cc_start: 0.8529 (p0) cc_final: 0.7733 (p0) REVERT: D 147 MET cc_start: 0.7853 (mpp) cc_final: 0.7283 (mtp) REVERT: D 226 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 227 MET cc_start: 0.7765 (mtt) cc_final: 0.7517 (mtt) REVERT: D 292 LEU cc_start: 0.8978 (mm) cc_final: 0.8505 (tp) REVERT: E 125 ASN cc_start: 0.8628 (t0) cc_final: 0.8036 (t0) REVERT: E 126 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8782 (tm-30) REVERT: E 133 ASP cc_start: 0.7722 (p0) cc_final: 0.7298 (p0) REVERT: E 217 GLU cc_start: 0.7620 (pm20) cc_final: 0.7360 (pm20) REVERT: E 243 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6958 (mt0) outliers start: 39 outliers final: 22 residues processed: 238 average time/residue: 0.1018 time to fit residues: 38.2644 Evaluate side-chains 231 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 LEU 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 219 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 153 ILE 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 136 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 0.0570 chunk 140 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.131510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101070 restraints weight = 40795.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102059 restraints weight = 22531.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103299 restraints weight = 17870.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104748 restraints weight = 12545.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105002 restraints weight = 10673.119| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1276 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= 0.145 Angle : 0.586 9.698 19302 Z= 0.296 Chirality : 0.044 0.194 2195 Planarity : 0.004 0.033 2411 Dihedral : 5.350 55.629 1969 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 2.87 % Allowed : 16.47 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.21), residues: 1695 helix: 1.80 (0.22), residues: 555 sheet: -0.89 (0.28), residues: 354 loop : -0.84 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.021 0.001 TYR B 301 PHE 0.033 0.001 PHE A 407 TRP 0.039 0.002 TRP A 239 HIS 0.001 0.000 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00330 (14170) covalent geometry : angle 0.57888 (19267) SS BOND : bond 0.00451 ( 10) SS BOND : angle 1.94734 ( 20) hydrogen bonds : bond 0.03691 ( 638) hydrogen bonds : angle 4.74548 ( 2046) link_NAG-ASN : bond 0.00466 ( 5) link_NAG-ASN : angle 2.57793 ( 15) *********************** 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 254 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8468 (ppp) cc_final: 0.7922 (ppp) REVERT: A 102 ASN cc_start: 0.8375 (p0) cc_final: 0.8060 (p0) REVERT: A 261 LEU cc_start: 0.8994 (tp) cc_final: 0.8522 (pp) REVERT: A 287 MET cc_start: 0.8108 (tpp) cc_final: 0.7503 (mmm) REVERT: B 103 GLU cc_start: 0.8567 (tt0) cc_final: 0.8347 (tt0) REVERT: B 188 LEU cc_start: 0.8990 (tp) cc_final: 0.8574 (pp) REVERT: B 195 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8581 (mt) REVERT: B 211 GLU cc_start: 0.7540 (tt0) cc_final: 0.7310 (tp30) REVERT: B 292 LEU cc_start: 0.9091 (tp) cc_final: 0.8466 (tt) REVERT: B 391 ARG cc_start: 0.6984 (mpp80) cc_final: 0.6330 (mmm160) REVERT: C 225 ILE cc_start: 0.9168 (tp) cc_final: 0.8852 (tp) REVERT: C 287 MET cc_start: 0.8059 (mmm) cc_final: 0.7544 (mmm) REVERT: D 102 ASN cc_start: 0.8529 (p0) cc_final: 0.7758 (p0) REVERT: D 147 MET cc_start: 0.8123 (mpp) cc_final: 0.7619 (mtp) REVERT: D 226 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8170 (tm-30) REVERT: D 227 MET cc_start: 0.7825 (mtt) cc_final: 0.7592 (mtt) REVERT: D 292 LEU cc_start: 0.8980 (mm) cc_final: 0.8473 (tp) REVERT: E 125 ASN cc_start: 0.8601 (t0) cc_final: 0.8015 (t0) REVERT: E 133 ASP cc_start: 0.7800 (p0) cc_final: 0.7531 (p0) REVERT: E 217 GLU cc_start: 0.7654 (pm20) cc_final: 0.7382 (pm20) REVERT: E 243 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: E 322 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7228 (mm) outliers start: 43 outliers final: 28 residues processed: 234 average time/residue: 0.1037 time to fit residues: 38.1272 Evaluate side-chains 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 224 LEU 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 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 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 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 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 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102447 restraints weight = 59684.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104046 restraints weight = 59461.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108091 restraints weight = 23393.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108262 restraints weight = 13717.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109268 restraints weight = 10986.749| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14185 Z= 0.198 Angle : 0.616 9.778 19302 Z= 0.312 Chirality : 0.044 0.192 2195 Planarity : 0.004 0.036 2411 Dihedral : 5.363 57.857 1967 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 3.13 % Allowed : 17.40 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.21), residues: 1695 helix: 1.95 (0.22), residues: 548 sheet: -1.00 (0.28), residues: 354 loop : -0.81 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 174 TYR 0.018 0.001 TYR C 223 PHE 0.017 0.001 PHE B 48 TRP 0.035 0.002 TRP A 239 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00459 (14170) covalent geometry : angle 0.60832 (19267) SS BOND : bond 0.00337 ( 10) SS BOND : angle 2.04814 ( 20) hydrogen bonds : bond 0.03732 ( 638) hydrogen bonds : angle 4.75949 ( 2046) link_NAG-ASN : bond 0.00464 ( 5) link_NAG-ASN : angle 2.57594 ( 15) *********************** 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 256 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8380 (p0) cc_final: 0.8117 (p0) REVERT: A 261 LEU cc_start: 0.8901 (tp) cc_final: 0.8453 (pp) REVERT: A 287 MET cc_start: 0.8234 (tpp) cc_final: 0.7647 (mmm) REVERT: B 188 LEU cc_start: 0.8934 (tp) cc_final: 0.8600 (pp) REVERT: B 195 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 252 ARG cc_start: 0.8546 (mtp180) cc_final: 0.8335 (mmm-85) REVERT: B 292 LEU cc_start: 0.9194 (tp) cc_final: 0.8520 (tt) REVERT: B 391 ARG cc_start: 0.6744 (mpp80) cc_final: 0.6244 (mmm160) REVERT: C 213 ARG cc_start: 0.8103 (mmt90) cc_final: 0.7748 (mtm110) REVERT: C 225 ILE cc_start: 0.9178 (tp) cc_final: 0.8869 (tp) REVERT: C 287 MET cc_start: 0.7901 (mmm) cc_final: 0.7513 (mmm) REVERT: D 102 ASN cc_start: 0.8550 (p0) cc_final: 0.7696 (p0) REVERT: D 147 MET cc_start: 0.8084 (mpp) cc_final: 0.7215 (mtp) REVERT: D 226 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8049 (tm-30) REVERT: D 292 LEU cc_start: 0.8913 (mm) cc_final: 0.8472 (tp) REVERT: D 409 ILE cc_start: 0.8819 (tp) cc_final: 0.8416 (tp) REVERT: D 412 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7356 (mp) REVERT: E 125 ASN cc_start: 0.8505 (t0) cc_final: 0.7986 (t0) REVERT: E 133 ASP cc_start: 0.7794 (p0) cc_final: 0.7588 (p0) REVERT: E 243 GLN cc_start: 0.7362 (pt0) cc_final: 0.7023 (mt0) REVERT: E 322 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7290 (mm) REVERT: E 324 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7773 (tm-30) outliers start: 47 outliers final: 37 residues processed: 236 average time/residue: 0.1007 time to fit residues: 37.1417 Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 291 LEU 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 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 299 LEU 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 233 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 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 167 LEU 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 13 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101793 restraints weight = 48358.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104984 restraints weight = 32396.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105366 restraints weight = 20936.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106958 restraints weight = 12317.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107598 restraints weight = 9897.445| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14185 Z= 0.156 Angle : 0.599 10.117 19302 Z= 0.303 Chirality : 0.044 0.192 2195 Planarity : 0.004 0.035 2411 Dihedral : 5.366 59.156 1967 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.16 % Rotamer: Outliers : 3.53 % Allowed : 17.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.21), residues: 1695 helix: 1.82 (0.22), residues: 554 sheet: -0.95 (0.28), residues: 354 loop : -0.85 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 174 TYR 0.022 0.001 TYR A 301 PHE 0.015 0.001 PHE B 410 TRP 0.033 0.002 TRP A 239 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00358 (14170) covalent geometry : angle 0.59267 (19267) SS BOND : bond 0.00338 ( 10) SS BOND : angle 1.80596 ( 20) hydrogen bonds : bond 0.03667 ( 638) hydrogen bonds : angle 4.70143 ( 2046) link_NAG-ASN : bond 0.00457 ( 5) link_NAG-ASN : angle 2.60173 ( 15) *********************** 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 259 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8493 (ppp) cc_final: 0.7960 (ppp) REVERT: A 102 ASN cc_start: 0.8381 (p0) cc_final: 0.8099 (p0) REVERT: A 261 LEU cc_start: 0.8960 (tp) cc_final: 0.8484 (pp) REVERT: A 263 MET cc_start: 0.8021 (mmm) cc_final: 0.7641 (ttm) REVERT: A 287 MET cc_start: 0.8173 (tpp) cc_final: 0.7557 (mmm) REVERT: B 188 LEU cc_start: 0.8963 (tp) cc_final: 0.8586 (pp) REVERT: B 195 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 292 LEU cc_start: 0.9161 (tp) cc_final: 0.8516 (tt) REVERT: B 391 ARG cc_start: 0.6906 (mpp80) cc_final: 0.6329 (mmm160) REVERT: C 213 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7908 (mtt180) REVERT: C 225 ILE cc_start: 0.9194 (tp) cc_final: 0.8879 (tp) REVERT: D 102 ASN cc_start: 0.8514 (p0) cc_final: 0.7712 (p0) REVERT: D 147 MET cc_start: 0.8173 (mpp) cc_final: 0.7377 (mtp) REVERT: D 226 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 227 MET cc_start: 0.7777 (mtt) cc_final: 0.7485 (mtt) REVERT: D 292 LEU cc_start: 0.8908 (mm) cc_final: 0.8423 (tp) REVERT: D 409 ILE cc_start: 0.8824 (tp) cc_final: 0.8430 (tp) REVERT: D 412 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7471 (mp) REVERT: E 125 ASN cc_start: 0.8562 (t0) cc_final: 0.7989 (t0) REVERT: E 126 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8744 (tm-30) REVERT: E 133 ASP cc_start: 0.7808 (p0) cc_final: 0.7539 (p0) REVERT: E 243 GLN cc_start: 0.7357 (pt0) cc_final: 0.6950 (mt0) REVERT: E 322 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7252 (mm) outliers start: 53 outliers final: 39 residues processed: 236 average time/residue: 0.0980 time to fit residues: 36.7654 Evaluate side-chains 239 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 220 MET Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 384 MET 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 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 278 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 233 LEU 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 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 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 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 98 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** E 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102373 restraints weight = 32586.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102854 restraints weight = 20361.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103927 restraints weight = 17350.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104581 restraints weight = 11867.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104917 restraints weight = 10441.142| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14185 Z= 0.115 Angle : 0.579 10.187 19302 Z= 0.291 Chirality : 0.043 0.192 2195 Planarity : 0.003 0.034 2411 Dihedral : 5.245 59.180 1967 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Rotamer: Outliers : 2.87 % Allowed : 18.53 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1695 helix: 1.82 (0.22), residues: 553 sheet: -0.79 (0.29), residues: 353 loop : -0.86 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 174 TYR 0.024 0.001 TYR D 301 PHE 0.015 0.001 PHE C 306 TRP 0.035 0.001 TRP A 239 HIS 0.001 0.000 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00251 (14170) covalent geometry : angle 0.57204 (19267) SS BOND : bond 0.00335 ( 10) SS BOND : angle 1.62352 ( 20) hydrogen bonds : bond 0.03475 ( 638) hydrogen bonds : angle 4.53604 ( 2046) link_NAG-ASN : bond 0.00475 ( 5) link_NAG-ASN : angle 2.62422 ( 15) *********************** 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 263 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8464 (ppp) cc_final: 0.7929 (ppp) REVERT: A 102 ASN cc_start: 0.8275 (p0) cc_final: 0.7974 (p0) REVERT: A 261 LEU cc_start: 0.8932 (tp) cc_final: 0.8480 (pp) REVERT: A 287 MET cc_start: 0.7961 (tpp) cc_final: 0.7332 (mmm) REVERT: B 103 GLU cc_start: 0.8463 (tt0) cc_final: 0.8098 (tt0) REVERT: B 188 LEU cc_start: 0.8905 (tp) cc_final: 0.8608 (pp) REVERT: B 211 GLU cc_start: 0.7362 (tp30) cc_final: 0.7114 (tp30) REVERT: B 252 ARG cc_start: 0.8500 (mtp180) cc_final: 0.8187 (mmm-85) REVERT: B 292 LEU cc_start: 0.9134 (tp) cc_final: 0.8494 (tt) REVERT: B 391 ARG cc_start: 0.6749 (mpp80) cc_final: 0.6241 (mmm160) REVERT: C 225 ILE cc_start: 0.9133 (tp) cc_final: 0.8809 (tp) REVERT: C 287 MET cc_start: 0.7422 (mmm) cc_final: 0.7065 (mmm) REVERT: C 296 SER cc_start: 0.8913 (p) cc_final: 0.8636 (t) REVERT: D 102 ASN cc_start: 0.8333 (p0) cc_final: 0.7552 (p0) REVERT: D 147 MET cc_start: 0.7980 (mpp) cc_final: 0.7233 (mtp) REVERT: D 226 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8108 (tm-30) REVERT: D 227 MET cc_start: 0.7621 (mtt) cc_final: 0.7401 (mtt) REVERT: D 292 LEU cc_start: 0.8896 (mm) cc_final: 0.8456 (tp) REVERT: D 409 ILE cc_start: 0.8760 (tp) cc_final: 0.8377 (tp) REVERT: D 412 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7604 (mp) REVERT: E 125 ASN cc_start: 0.8452 (t0) cc_final: 0.7911 (t0) REVERT: E 126 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8718 (tm-30) REVERT: E 133 ASP cc_start: 0.7498 (p0) cc_final: 0.7226 (p0) REVERT: E 243 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6970 (mt0) outliers start: 43 outliers final: 29 residues processed: 239 average time/residue: 0.0969 time to fit residues: 36.5577 Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 402 CYS 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 291 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 220 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL 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 115 CYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 243 GLN 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 4 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101306 restraints weight = 38521.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102154 restraints weight = 23295.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103390 restraints weight = 19060.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104035 restraints weight = 13330.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104615 restraints weight = 11859.436| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14185 Z= 0.135 Angle : 0.594 10.173 19302 Z= 0.298 Chirality : 0.044 0.193 2195 Planarity : 0.003 0.033 2411 Dihedral : 5.239 59.222 1967 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.16 % Rotamer: Outliers : 2.87 % Allowed : 18.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.21), residues: 1695 helix: 1.84 (0.22), residues: 554 sheet: -0.75 (0.29), residues: 348 loop : -0.87 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 174 TYR 0.025 0.001 TYR B 222 PHE 0.013 0.001 PHE A 407 TRP 0.033 0.002 TRP A 239 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00309 (14170) covalent geometry : angle 0.58611 (19267) SS BOND : bond 0.00524 ( 10) SS BOND : angle 2.07061 ( 20) hydrogen bonds : bond 0.03439 ( 638) hydrogen bonds : angle 4.50741 ( 2046) link_NAG-ASN : bond 0.00465 ( 5) link_NAG-ASN : angle 2.57285 ( 15) *********************** 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 250 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8267 (p0) cc_final: 0.7974 (p0) REVERT: A 195 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 261 LEU cc_start: 0.8949 (tp) cc_final: 0.8440 (pp) REVERT: A 287 MET cc_start: 0.7840 (tpp) cc_final: 0.7515 (mmm) REVERT: B 103 GLU cc_start: 0.8416 (tt0) cc_final: 0.8089 (tt0) REVERT: B 188 LEU cc_start: 0.8901 (tp) cc_final: 0.8608 (pp) REVERT: B 211 GLU cc_start: 0.7384 (tp30) cc_final: 0.7141 (tp30) REVERT: B 252 ARG cc_start: 0.8505 (mtp180) cc_final: 0.8183 (mmm-85) REVERT: B 292 LEU cc_start: 0.9122 (tp) cc_final: 0.8503 (tt) REVERT: B 391 ARG cc_start: 0.6767 (mpp80) cc_final: 0.6263 (mmm160) REVERT: C 225 ILE cc_start: 0.9159 (tp) cc_final: 0.8828 (tp) REVERT: C 287 MET cc_start: 0.7480 (mmm) cc_final: 0.7081 (mmm) REVERT: C 296 SER cc_start: 0.8903 (p) cc_final: 0.8622 (t) REVERT: D 102 ASN cc_start: 0.8362 (p0) cc_final: 0.7539 (p0) REVERT: D 147 MET cc_start: 0.8012 (mpp) cc_final: 0.7215 (mtp) REVERT: D 226 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8084 (tm-30) REVERT: D 292 LEU cc_start: 0.8881 (mm) cc_final: 0.8447 (tp) REVERT: D 409 ILE cc_start: 0.8781 (tp) cc_final: 0.8421 (tp) REVERT: E 125 ASN cc_start: 0.8465 (t0) cc_final: 0.7921 (t0) REVERT: E 133 ASP cc_start: 0.7674 (p0) cc_final: 0.7250 (p0) REVERT: E 243 GLN cc_start: 0.7358 (pt0) cc_final: 0.7005 (mt0) REVERT: E 322 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7210 (mm) outliers start: 43 outliers final: 34 residues processed: 233 average time/residue: 0.0947 time to fit residues: 34.9081 Evaluate side-chains 239 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 114 ASP 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 291 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 154 MET 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 280 VAL 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 412 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 0.0470 chunk 162 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102965 restraints weight = 44272.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105403 restraints weight = 26481.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105630 restraints weight = 21823.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107698 restraints weight = 12826.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.109650 restraints weight = 9881.406| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1792 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= 0.119 Angle : 0.583 10.263 19302 Z= 0.292 Chirality : 0.043 0.192 2195 Planarity : 0.003 0.033 2411 Dihedral : 5.181 59.469 1967 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.25 % Favored : 96.63 % Rotamer: Outliers : 2.73 % Allowed : 18.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1695 helix: 1.83 (0.22), residues: 554 sheet: -0.64 (0.29), residues: 346 loop : -0.87 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 174 TYR 0.019 0.001 TYR D 301 PHE 0.016 0.001 PHE C 306 TRP 0.034 0.001 TRP C 239 HIS 0.001 0.000 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00267 (14170) covalent geometry : angle 0.57601 (19267) SS BOND : bond 0.00341 ( 10) SS BOND : angle 1.91810 ( 20) hydrogen bonds : bond 0.03307 ( 638) hydrogen bonds : angle 4.43834 ( 2046) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 2.59940 ( 15) *********************** 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 259 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8400 (p0) cc_final: 0.8099 (p0) REVERT: A 195 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8048 (mt) REVERT: A 261 LEU cc_start: 0.9011 (tp) cc_final: 0.8519 (pp) REVERT: B 103 GLU cc_start: 0.8528 (tt0) cc_final: 0.8234 (tt0) REVERT: B 188 LEU cc_start: 0.8950 (tp) cc_final: 0.8616 (pp) REVERT: B 211 GLU cc_start: 0.7508 (tp30) cc_final: 0.7189 (tp30) REVERT: B 292 LEU cc_start: 0.9091 (tp) cc_final: 0.8503 (tt) REVERT: B 391 ARG cc_start: 0.6982 (mpp80) cc_final: 0.6344 (mmm160) REVERT: C 225 ILE cc_start: 0.9136 (tp) cc_final: 0.8807 (tp) REVERT: C 287 MET cc_start: 0.7705 (mmm) cc_final: 0.7306 (mmm) REVERT: D 102 ASN cc_start: 0.8485 (p0) cc_final: 0.7675 (p0) REVERT: D 147 MET cc_start: 0.8155 (mpp) cc_final: 0.7427 (mtp) REVERT: D 226 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8110 (tm-30) REVERT: D 292 LEU cc_start: 0.8898 (mm) cc_final: 0.8399 (tp) REVERT: D 409 ILE cc_start: 0.8871 (tp) cc_final: 0.8510 (tp) REVERT: E 125 ASN cc_start: 0.8553 (t0) cc_final: 0.7962 (t0) REVERT: E 133 ASP cc_start: 0.7756 (p0) cc_final: 0.7351 (p0) REVERT: E 243 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.7008 (mt0) REVERT: E 322 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7222 (mm) outliers start: 41 outliers final: 33 residues processed: 241 average time/residue: 0.0936 time to fit residues: 35.8803 Evaluate side-chains 245 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 220 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 402 CYS 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 240 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 154 MET 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 154 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 16 optimal weight: 0.0070 chunk 129 optimal weight: 0.0470 chunk 141 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.134041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105199 restraints weight = 55744.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107336 restraints weight = 38157.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108337 restraints weight = 23285.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110507 restraints weight = 13547.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112997 restraints weight = 10193.670| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14185 Z= 0.110 Angle : 0.593 10.501 19302 Z= 0.294 Chirality : 0.043 0.189 2195 Planarity : 0.003 0.033 2411 Dihedral : 5.125 59.199 1967 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 2.53 % Allowed : 19.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1695 helix: 1.77 (0.22), residues: 561 sheet: -0.48 (0.30), residues: 346 loop : -0.84 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 174 TYR 0.020 0.001 TYR D 301 PHE 0.036 0.001 PHE B 145 TRP 0.038 0.002 TRP C 239 HIS 0.001 0.000 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00240 (14170) covalent geometry : angle 0.58568 (19267) SS BOND : bond 0.00350 ( 10) SS BOND : angle 1.81554 ( 20) hydrogen bonds : bond 0.03254 ( 638) hydrogen bonds : angle 4.36983 ( 2046) link_NAG-ASN : bond 0.00481 ( 5) link_NAG-ASN : angle 2.61504 ( 15) ********************** 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 259 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8356 (p0) cc_final: 0.8035 (p0) REVERT: A 195 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 261 LEU cc_start: 0.8984 (tp) cc_final: 0.8484 (pp) REVERT: B 103 GLU cc_start: 0.8532 (tt0) cc_final: 0.8305 (tt0) REVERT: B 188 LEU cc_start: 0.8930 (tp) cc_final: 0.8639 (pp) REVERT: B 211 GLU cc_start: 0.7401 (tp30) cc_final: 0.7045 (tp30) REVERT: B 292 LEU cc_start: 0.9082 (tp) cc_final: 0.8497 (tt) REVERT: C 225 ILE cc_start: 0.9091 (tp) cc_final: 0.8757 (tp) REVERT: C 287 MET cc_start: 0.7625 (mmm) cc_final: 0.7157 (mmm) REVERT: C 412 ILE cc_start: 0.9120 (tp) cc_final: 0.8754 (tp) REVERT: D 102 ASN cc_start: 0.8415 (p0) cc_final: 0.7557 (p0) REVERT: D 147 MET cc_start: 0.8056 (mpp) cc_final: 0.7346 (mtp) REVERT: D 292 LEU cc_start: 0.8889 (mm) cc_final: 0.8394 (tp) REVERT: D 409 ILE cc_start: 0.8855 (tp) cc_final: 0.8494 (tp) REVERT: E 125 ASN cc_start: 0.8529 (t0) cc_final: 0.7925 (t0) REVERT: E 133 ASP cc_start: 0.7714 (p0) cc_final: 0.7323 (p0) REVERT: E 243 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: E 322 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7195 (mm) outliers start: 38 outliers final: 30 residues processed: 244 average time/residue: 0.0905 time to fit residues: 35.4907 Evaluate side-chains 243 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 220 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 402 CYS 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 240 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 154 MET 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 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 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 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 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 99 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 16 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.6792 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.132110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100955 restraints weight = 34707.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101868 restraints weight = 23350.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102520 restraints weight = 15976.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103882 restraints weight = 12299.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104065 restraints weight = 10188.161| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1943 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= 0.150 Angle : 0.605 10.353 19302 Z= 0.305 Chirality : 0.044 0.189 2195 Planarity : 0.003 0.033 2411 Dihedral : 5.172 59.978 1967 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 2.53 % Allowed : 19.80 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.21), residues: 1695 helix: 1.79 (0.22), residues: 562 sheet: -0.55 (0.29), residues: 347 loop : -0.85 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 391 TYR 0.029 0.001 TYR C 301 PHE 0.032 0.001 PHE B 145 TRP 0.041 0.002 TRP D 239 HIS 0.002 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00346 (14170) covalent geometry : angle 0.59844 (19267) SS BOND : bond 0.00328 ( 10) SS BOND : angle 1.86033 ( 20) hydrogen bonds : bond 0.03374 ( 638) hydrogen bonds : angle 4.45393 ( 2046) link_NAG-ASN : bond 0.00472 ( 5) link_NAG-ASN : angle 2.53041 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.12 seconds wall clock time: 39 minutes 46.46 seconds (2386.46 seconds total)