Starting phenix.real_space_refine on Tue May 20 03:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gat_29907/05_2025/8gat_29907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gat_29907/05_2025/8gat_29907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gat_29907/05_2025/8gat_29907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gat_29907/05_2025/8gat_29907.map" model { file = "/net/cci-nas-00/data/ceres_data/8gat_29907/05_2025/8gat_29907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gat_29907/05_2025/8gat_29907.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 112 5.16 5 C 12228 2.51 5 N 3368 2.21 5 O 3788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19496 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2987 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Restraints were copied for chains: G, J, N, B, E, H, F, I, M Time building chain proxies: 8.31, per 1000 atoms: 0.43 Number of scatterers: 19496 At special positions: 0 Unit cell: (147.63, 147.63, 87.69, 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 112 16.00 O 3788 8.00 N 3368 7.00 C 12228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.03 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " 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 200 " " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 367 " " NAG A 504 " - " ASN A 234 " " NAG B 501 " - " ASN B 200 " " NAG B 502 " - " ASN B 146 " " NAG B 503 " - " ASN B 367 " " NAG B 504 " - " ASN B 234 " " NAG E 501 " - " ASN E 200 " " NAG E 502 " - " ASN E 146 " " NAG E 503 " - " ASN E 367 " " NAG E 504 " - " ASN E 234 " " NAG H 501 " - " ASN H 200 " " NAG H 502 " - " ASN H 146 " " NAG H 503 " - " ASN H 367 " " NAG H 504 " - " ASN H 234 " Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 2.3 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 56 sheets defined 3.2% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.764A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 removed outlier: 4.011A pdb=" N MET A 467 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.970A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.764A pdb=" N ASN B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 removed outlier: 4.011A pdb=" N MET B 467 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.970A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.764A pdb=" N ASN E 146 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 467 removed outlier: 4.011A pdb=" N MET E 467 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.970A pdb=" N LYS F 64 " --> pdb=" O ASP F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'H' and resid 104 through 109 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.764A pdb=" N ASN H 146 " --> pdb=" O GLY H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 467 removed outlier: 4.011A pdb=" N MET H 467 " --> pdb=" O ILE H 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.970A pdb=" N LYS I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing sheet with id=1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.991A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 408 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.997A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 133 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.772A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 203 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.523A pdb=" N THR A 236 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.680A pdb=" N THR A 252 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 254 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.075A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS A 280 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.856A pdb=" N LEU A 372 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU A 399 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=9, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.558A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU M 18 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU M 78 " --> pdb=" O CYS M 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP M 72 " --> pdb=" O SER M 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER M 70 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.625A pdb=" N ILE N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=14, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.697A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.991A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 408 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.997A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 133 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.772A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 203 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE B 205 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.523A pdb=" N THR B 236 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 223 through 224 removed outlier: 7.680A pdb=" N THR B 252 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 254 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE B 256 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.075A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 280 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.856A pdb=" N LEU B 372 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU B 399 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 378 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'B' and resid 428 through 429 Processing sheet with id=23, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.558A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 18 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP C 72 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 79 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.625A pdb=" N ILE D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=28, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.697A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.991A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 408 " --> pdb=" O TYR E 423 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.997A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 133 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 179 through 184 removed outlier: 3.772A pdb=" N SER E 179 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA E 203 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER E 214 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE E 205 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'E' and resid 223 through 224 removed outlier: 3.523A pdb=" N THR E 236 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'E' and resid 223 through 224 removed outlier: 7.680A pdb=" N THR E 252 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR E 267 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 254 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE E 265 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE E 256 " --> pdb=" O VAL E 263 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.075A pdb=" N CYS E 278 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL E 290 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS E 280 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG E 288 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY E 286 " --> pdb=" O PRO E 282 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 353 through 356 removed outlier: 6.856A pdb=" N LEU E 372 " --> pdb=" O GLU E 399 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU E 399 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR E 374 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS E 378 " --> pdb=" O ASN E 393 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN E 393 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'E' and resid 428 through 429 Processing sheet with id=37, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.558A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 18 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 78 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP F 72 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR F 79 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.625A pdb=" N ILE G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=42, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.697A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.991A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY H 408 " --> pdb=" O TYR H 423 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.997A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA H 133 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'H' and resid 179 through 184 removed outlier: 3.772A pdb=" N SER H 179 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA H 203 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 214 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE H 205 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'H' and resid 223 through 224 removed outlier: 3.523A pdb=" N THR H 236 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL H 231 " --> pdb=" O THR H 238 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'H' and resid 223 through 224 removed outlier: 7.680A pdb=" N THR H 252 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR H 267 " --> pdb=" O THR H 252 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE H 254 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE H 265 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE H 256 " --> pdb=" O VAL H 263 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.075A pdb=" N CYS H 278 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL H 290 " --> pdb=" O CYS H 278 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS H 280 " --> pdb=" O ARG H 288 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG H 288 " --> pdb=" O CYS H 280 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY H 286 " --> pdb=" O PRO H 282 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'H' and resid 353 through 356 removed outlier: 6.856A pdb=" N LEU H 372 " --> pdb=" O GLU H 399 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU H 399 " --> pdb=" O LEU H 372 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR H 374 " --> pdb=" O ILE H 397 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS H 378 " --> pdb=" O ASN H 393 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN H 393 " --> pdb=" O LYS H 378 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'H' and resid 428 through 429 Processing sheet with id=51, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.558A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 18 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP I 72 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR I 79 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.810A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.625A pdb=" N ILE J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=56, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.697A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1620 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: 7.41 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5052 1.33 - 1.46: 5140 1.46 - 1.58: 9644 1.58 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 19972 Sorted by residual: bond pdb=" N ILE I 56 " pdb=" CA ILE I 56 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ILE M 56 " pdb=" CA ILE M 56 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ILE F 56 " pdb=" CA ILE F 56 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ILE C 56 " pdb=" CA ILE C 56 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" C ILE I 56 " pdb=" O ILE I 56 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.19e-02 7.06e+03 7.16e+00 ... (remaining 19967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 26356 2.48 - 4.95: 636 4.95 - 7.43: 84 7.43 - 9.91: 20 9.91 - 12.38: 16 Bond angle restraints: 27112 Sorted by residual: angle pdb=" C ILE I 56 " pdb=" N THR I 57 " pdb=" CA THR I 57 " ideal model delta sigma weight residual 122.81 110.43 12.38 1.68e+00 3.54e-01 5.43e+01 angle pdb=" C ILE C 56 " pdb=" N THR C 57 " pdb=" CA THR C 57 " ideal model delta sigma weight residual 122.81 110.43 12.38 1.68e+00 3.54e-01 5.43e+01 angle pdb=" C ILE F 56 " pdb=" N THR F 57 " pdb=" CA THR F 57 " ideal model delta sigma weight residual 122.81 110.43 12.38 1.68e+00 3.54e-01 5.43e+01 angle pdb=" C ILE M 56 " pdb=" N THR M 57 " pdb=" CA THR M 57 " ideal model delta sigma weight residual 122.81 110.43 12.38 1.68e+00 3.54e-01 5.43e+01 angle pdb=" C ASP C 55 " pdb=" N ILE C 56 " pdb=" CA ILE C 56 " ideal model delta sigma weight residual 121.97 132.34 -10.37 1.80e+00 3.09e-01 3.32e+01 ... (remaining 27107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.34: 11532 20.34 - 40.67: 300 40.67 - 61.01: 76 61.01 - 81.34: 12 81.34 - 101.68: 32 Dihedral angle restraints: 11952 sinusoidal: 4908 harmonic: 7044 Sorted by residual: dihedral pdb=" CB CYS E 318 " pdb=" SG CYS E 318 " pdb=" SG CYS E 337 " pdb=" CB CYS E 337 " ideal model delta sinusoidal sigma weight residual 93.00 146.03 -53.03 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 146.03 -53.03 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS H 318 " pdb=" SG CYS H 318 " pdb=" SG CYS H 337 " pdb=" CB CYS H 337 " ideal model delta sinusoidal sigma weight residual 93.00 146.03 -53.03 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 11949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2520 0.088 - 0.177: 408 0.177 - 0.265: 16 0.265 - 0.353: 4 0.353 - 0.441: 4 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA ASN I 53 " pdb=" N ASN I 53 " pdb=" C ASN I 53 " pdb=" CB ASN I 53 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ASN F 53 " pdb=" N ASN F 53 " pdb=" C ASN F 53 " pdb=" CB ASN F 53 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ASN M 53 " pdb=" N ASN M 53 " pdb=" C ASN M 53 " pdb=" CB ASN M 53 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 2949 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 52A" -0.029 2.00e-02 2.50e+03 1.82e-02 8.27e+00 pdb=" CG TRP M 52A" 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP M 52A" -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP M 52A" 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP M 52A" -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP M 52A" 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP M 52A" -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 52A" -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 52A" -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP M 52A" 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 52A" -0.029 2.00e-02 2.50e+03 1.82e-02 8.27e+00 pdb=" CG TRP C 52A" 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 52A" -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 52A" 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP C 52A" -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 52A" 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 52A" -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 52A" -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 52A" -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 52A" 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 52A" -0.029 2.00e-02 2.50e+03 1.82e-02 8.27e+00 pdb=" CG TRP F 52A" 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP F 52A" -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP F 52A" 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP F 52A" -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP F 52A" 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP F 52A" -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 52A" -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 52A" -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP F 52A" 0.002 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 80 2.51 - 3.11: 12536 3.11 - 3.70: 27140 3.70 - 4.30: 40240 4.30 - 4.90: 71028 Nonbonded interactions: 151024 Sorted by model distance: nonbonded pdb=" NZ LYS A 415 " pdb=" OE1 GLU H 259 " model vdw 1.911 3.120 nonbonded pdb=" OE1 GLU A 259 " pdb=" NZ LYS B 415 " model vdw 1.911 3.120 nonbonded pdb=" OE1 GLU E 259 " pdb=" NZ LYS H 415 " model vdw 1.911 3.120 nonbonded pdb=" OE1 GLU B 259 " pdb=" NZ LYS E 415 " model vdw 1.911 3.120 nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " model vdw 2.037 3.760 ... (remaining 151019 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: 0.16 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 41.450 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.006 0.056 20024 Z= 0.281 Angle : 0.991 12.384 27232 Z= 0.550 Chirality : 0.062 0.441 2952 Planarity : 0.007 0.061 3476 Dihedral : 12.165 101.679 7380 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.64 % Favored : 92.20 % Rotamer: Outliers : 0.75 % Allowed : 2.83 % Favored : 96.42 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.14), residues: 2460 helix: -3.83 (0.58), residues: 24 sheet: -1.40 (0.16), residues: 888 loop : -3.25 (0.11), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP M 52A HIS 0.007 0.002 HIS B 191 PHE 0.025 0.004 PHE B 410 TYR 0.025 0.003 TYR B 406 ARG 0.009 0.001 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 16) link_NAG-ASN : angle 3.26198 ( 48) hydrogen bonds : bond 0.27894 ( 552) hydrogen bonds : angle 9.73451 ( 1620) SS BOND : bond 0.00214 ( 36) SS BOND : angle 1.59298 ( 72) covalent geometry : bond 0.00599 (19972) covalent geometry : angle 0.97982 (27112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 547 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 SER cc_start: 0.8213 (p) cc_final: 0.8012 (t) REVERT: A 432 GLU cc_start: 0.6877 (mp0) cc_final: 0.6596 (mp0) REVERT: A 457 SER cc_start: 0.8432 (t) cc_final: 0.8189 (m) REVERT: A 464 ILE cc_start: 0.8080 (pt) cc_final: 0.7789 (OUTLIER) REVERT: M 28 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6641 (ttpp) REVERT: M 49 SER cc_start: 0.7979 (p) cc_final: 0.7741 (t) REVERT: M 91 TYR cc_start: 0.8073 (m-80) cc_final: 0.7827 (m-80) REVERT: N 82 ASP cc_start: 0.8279 (m-30) cc_final: 0.7970 (m-30) REVERT: N 102 THR cc_start: 0.8250 (m) cc_final: 0.7956 (p) REVERT: B 362 MET cc_start: 0.8559 (ptm) cc_final: 0.7944 (ptp) REVERT: B 393 ASN cc_start: 0.8279 (m110) cc_final: 0.8008 (m110) REVERT: B 457 SER cc_start: 0.8456 (t) cc_final: 0.8240 (m) REVERT: B 464 ILE cc_start: 0.8072 (pt) cc_final: 0.7783 (OUTLIER) REVERT: C 28 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6509 (ttpp) REVERT: C 59 TYR cc_start: 0.8575 (m-10) cc_final: 0.8364 (m-80) REVERT: C 78 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7416 (tm) REVERT: D 56 SER cc_start: 0.7823 (t) cc_final: 0.7530 (p) REVERT: D 63 SER cc_start: 0.7874 (m) cc_final: 0.7525 (p) REVERT: D 82 ASP cc_start: 0.8179 (m-30) cc_final: 0.7963 (m-30) REVERT: D 102 THR cc_start: 0.8180 (m) cc_final: 0.7838 (p) REVERT: E 109 SER cc_start: 0.8268 (p) cc_final: 0.8065 (t) REVERT: E 147 ASN cc_start: 0.7749 (m-40) cc_final: 0.7403 (m110) REVERT: E 210 ARG cc_start: 0.8302 (ptp90) cc_final: 0.8084 (ptp-110) REVERT: E 393 ASN cc_start: 0.8265 (m110) cc_final: 0.8009 (m110) REVERT: E 432 GLU cc_start: 0.6924 (mp0) cc_final: 0.6573 (mp0) REVERT: E 457 SER cc_start: 0.8389 (t) cc_final: 0.8188 (m) REVERT: E 464 ILE cc_start: 0.8116 (pt) cc_final: 0.7833 (OUTLIER) REVERT: F 28 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6477 (ttpp) REVERT: F 49 SER cc_start: 0.8195 (p) cc_final: 0.7918 (t) REVERT: F 56 ILE cc_start: 0.8445 (mt) cc_final: 0.8241 (mt) REVERT: F 78 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7521 (tm) REVERT: G 102 THR cc_start: 0.8183 (m) cc_final: 0.7848 (p) REVERT: H 109 SER cc_start: 0.8283 (p) cc_final: 0.8062 (t) REVERT: H 147 ASN cc_start: 0.7880 (m-40) cc_final: 0.7543 (m110) REVERT: H 210 ARG cc_start: 0.8368 (ptp90) cc_final: 0.8152 (ptp-110) REVERT: H 362 MET cc_start: 0.8618 (ptm) cc_final: 0.8299 (ptm) REVERT: H 457 SER cc_start: 0.8356 (t) cc_final: 0.8140 (m) REVERT: H 464 ILE cc_start: 0.8130 (pt) cc_final: 0.7811 (OUTLIER) REVERT: I 28 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6624 (ttpp) REVERT: I 49 SER cc_start: 0.8059 (p) cc_final: 0.7784 (t) REVERT: I 78 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7518 (tm) REVERT: I 91 TYR cc_start: 0.8095 (m-80) cc_final: 0.7814 (m-80) REVERT: I 100 THR cc_start: 0.8514 (p) cc_final: 0.8279 (p) REVERT: J 93 SER cc_start: 0.7813 (p) cc_final: 0.7462 (p) outliers start: 16 outliers final: 9 residues processed: 563 average time/residue: 1.2309 time to fit residues: 783.6958 Evaluate side-chains 479 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 467 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 52 TRP Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 78 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 199 ASN A 226 GLN A 342 ASN A 393 ASN A 395 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 184 HIS B 199 ASN B 226 GLN B 395 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN E 93 ASN E 184 HIS E 226 GLN E 395 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 HIS H 226 GLN H 342 ASN H 393 ASN H 395 GLN ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093033 restraints weight = 27796.542| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.87 r_work: 0.2992 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20024 Z= 0.160 Angle : 0.657 7.688 27232 Z= 0.345 Chirality : 0.046 0.187 2952 Planarity : 0.005 0.053 3476 Dihedral : 8.437 57.498 3080 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.67 % Favored : 93.17 % Rotamer: Outliers : 3.11 % Allowed : 11.32 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.14), residues: 2460 helix: -2.89 (0.65), residues: 24 sheet: -0.74 (0.17), residues: 884 loop : -2.96 (0.12), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 295 HIS 0.003 0.001 HIS E 184 PHE 0.022 0.002 PHE E 410 TYR 0.014 0.002 TYR E 121 ARG 0.004 0.001 ARG E 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 16) link_NAG-ASN : angle 2.37039 ( 48) hydrogen bonds : bond 0.04651 ( 552) hydrogen bonds : angle 6.42413 ( 1620) SS BOND : bond 0.00158 ( 36) SS BOND : angle 1.14754 ( 72) covalent geometry : bond 0.00371 (19972) covalent geometry : angle 0.64792 (27112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 497 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 SER cc_start: 0.8380 (m) cc_final: 0.8115 (p) REVERT: A 356 ASP cc_start: 0.8111 (t0) cc_final: 0.7850 (t0) REVERT: A 392 THR cc_start: 0.8433 (p) cc_final: 0.8201 (m) REVERT: A 431 LYS cc_start: 0.7979 (tppt) cc_final: 0.7619 (tppt) REVERT: A 435 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8442 (mtmt) REVERT: A 457 SER cc_start: 0.8536 (t) cc_final: 0.8312 (m) REVERT: A 464 ILE cc_start: 0.8174 (pt) cc_final: 0.7779 (OUTLIER) REVERT: M 28 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7802 (ttmm) REVERT: M 37 VAL cc_start: 0.8224 (t) cc_final: 0.8006 (t) REVERT: N 89 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: N 92 ASP cc_start: 0.8323 (t0) cc_final: 0.7922 (t0) REVERT: N 95 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7549 (pp) REVERT: B 147 ASN cc_start: 0.8028 (m-40) cc_final: 0.7777 (m110) REVERT: B 247 SER cc_start: 0.8314 (m) cc_final: 0.8032 (p) REVERT: B 362 MET cc_start: 0.8566 (ptm) cc_final: 0.8055 (ptp) REVERT: B 393 ASN cc_start: 0.8469 (m110) cc_final: 0.8128 (m-40) REVERT: B 457 SER cc_start: 0.8568 (t) cc_final: 0.8355 (m) REVERT: B 464 ILE cc_start: 0.8193 (pt) cc_final: 0.7948 (OUTLIER) REVERT: C 28 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7618 (ttmm) REVERT: C 78 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7862 (tm) REVERT: D 46 LEU cc_start: 0.8724 (tp) cc_final: 0.8464 (tp) REVERT: D 89 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: D 92 ASP cc_start: 0.8300 (t0) cc_final: 0.7925 (t0) REVERT: D 93 SER cc_start: 0.8164 (p) cc_final: 0.7848 (p) REVERT: D 95 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7402 (pp) REVERT: E 147 ASN cc_start: 0.8076 (m-40) cc_final: 0.7744 (m110) REVERT: E 210 ARG cc_start: 0.8394 (ptp90) cc_final: 0.8110 (ptp-110) REVERT: E 393 ASN cc_start: 0.8478 (m110) cc_final: 0.8072 (m-40) REVERT: E 432 GLU cc_start: 0.7692 (mp0) cc_final: 0.7271 (mp0) REVERT: E 457 SER cc_start: 0.8501 (t) cc_final: 0.8285 (m) REVERT: E 464 ILE cc_start: 0.8173 (pt) cc_final: 0.7886 (OUTLIER) REVERT: F 28 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7618 (ttpp) REVERT: F 56 ILE cc_start: 0.8723 (mt) cc_final: 0.8484 (mt) REVERT: G 77 SER cc_start: 0.8103 (t) cc_final: 0.7509 (p) REVERT: G 95 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7765 (pp) REVERT: H 113 ASP cc_start: 0.7451 (m-30) cc_final: 0.7213 (m-30) REVERT: H 147 ASN cc_start: 0.8221 (m-40) cc_final: 0.7877 (m110) REVERT: H 210 ARG cc_start: 0.8462 (ptp90) cc_final: 0.8177 (ptp-110) REVERT: H 247 SER cc_start: 0.8284 (m) cc_final: 0.8000 (p) REVERT: H 356 ASP cc_start: 0.8146 (t0) cc_final: 0.7935 (t0) REVERT: H 457 SER cc_start: 0.8499 (t) cc_final: 0.8279 (m) REVERT: H 464 ILE cc_start: 0.8210 (pt) cc_final: 0.7918 (OUTLIER) REVERT: I 28 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7763 (ttpp) REVERT: I 46 GLU cc_start: 0.8298 (tt0) cc_final: 0.8096 (tt0) REVERT: I 78 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7993 (tm) REVERT: J 46 LEU cc_start: 0.8736 (tp) cc_final: 0.8507 (tp) REVERT: J 77 SER cc_start: 0.8057 (t) cc_final: 0.7432 (p) REVERT: J 89 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: J 95 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7667 (pp) outliers start: 66 outliers final: 25 residues processed: 537 average time/residue: 1.0891 time to fit residues: 669.8502 Evaluate side-chains 479 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 445 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 147 ASN A 184 HIS A 199 ASN A 226 GLN A 441 ASN A 465 ASN B 93 ASN B 136 GLN B 199 ASN B 441 ASN D 55 GLN E 93 ASN E 199 ASN E 226 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN H 86 ASN H 441 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091210 restraints weight = 27993.324| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.88 r_work: 0.2978 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20024 Z= 0.160 Angle : 0.619 6.592 27232 Z= 0.327 Chirality : 0.046 0.139 2952 Planarity : 0.005 0.049 3476 Dihedral : 5.922 50.616 3068 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.38 % Favored : 93.46 % Rotamer: Outliers : 4.20 % Allowed : 13.40 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.15), residues: 2460 helix: -1.62 (0.78), residues: 24 sheet: -0.24 (0.18), residues: 868 loop : -2.74 (0.12), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 178 HIS 0.003 0.001 HIS E 184 PHE 0.018 0.002 PHE E 410 TYR 0.019 0.002 TYR E 121 ARG 0.004 0.001 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 16) link_NAG-ASN : angle 2.39328 ( 48) hydrogen bonds : bond 0.04384 ( 552) hydrogen bonds : angle 5.94192 ( 1620) SS BOND : bond 0.00216 ( 36) SS BOND : angle 0.98809 ( 72) covalent geometry : bond 0.00377 (19972) covalent geometry : angle 0.60953 (27112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 453 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 VAL cc_start: 0.8259 (p) cc_final: 0.8038 (t) REVERT: A 247 SER cc_start: 0.8389 (m) cc_final: 0.8165 (p) REVERT: A 356 ASP cc_start: 0.8087 (t0) cc_final: 0.7861 (t0) REVERT: A 435 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8477 (mtmt) REVERT: A 457 SER cc_start: 0.8508 (t) cc_final: 0.8298 (m) REVERT: A 464 ILE cc_start: 0.8166 (pt) cc_final: 0.7878 (OUTLIER) REVERT: M 37 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.8029 (t) REVERT: N 45 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.8035 (t0) REVERT: N 92 ASP cc_start: 0.8357 (t0) cc_final: 0.7928 (t0) REVERT: N 95 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7569 (pp) REVERT: B 102 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8428 (tttp) REVERT: B 119 GLU cc_start: 0.7883 (mp0) cc_final: 0.7445 (mp0) REVERT: B 147 ASN cc_start: 0.8025 (m-40) cc_final: 0.7722 (m110) REVERT: B 213 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: B 239 VAL cc_start: 0.8251 (p) cc_final: 0.8042 (t) REVERT: B 247 SER cc_start: 0.8340 (m) cc_final: 0.8088 (p) REVERT: B 362 MET cc_start: 0.8566 (ptm) cc_final: 0.8084 (ptp) REVERT: B 391 GLN cc_start: 0.8403 (pt0) cc_final: 0.8093 (pt0) REVERT: B 393 ASN cc_start: 0.8531 (m110) cc_final: 0.8224 (m-40) REVERT: B 457 SER cc_start: 0.8541 (t) cc_final: 0.8336 (m) REVERT: B 464 ILE cc_start: 0.8136 (pt) cc_final: 0.7931 (mm) REVERT: D 46 LEU cc_start: 0.8698 (tp) cc_final: 0.8412 (tp) REVERT: D 77 SER cc_start: 0.7812 (t) cc_final: 0.7589 (t) REVERT: D 89 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: D 92 ASP cc_start: 0.8313 (t0) cc_final: 0.7835 (t0) REVERT: D 93 SER cc_start: 0.8163 (p) cc_final: 0.7837 (p) REVERT: D 95 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7372 (pp) REVERT: E 102 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8414 (tttp) REVERT: E 147 ASN cc_start: 0.8086 (m-40) cc_final: 0.7746 (m110) REVERT: E 210 ARG cc_start: 0.8377 (ptp90) cc_final: 0.8142 (ptp-110) REVERT: E 239 VAL cc_start: 0.8195 (p) cc_final: 0.7992 (t) REVERT: E 393 ASN cc_start: 0.8485 (m110) cc_final: 0.8102 (m-40) REVERT: E 432 GLU cc_start: 0.7697 (mp0) cc_final: 0.7313 (mp0) REVERT: F 100 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7745 (ttp-170) REVERT: G 95 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7848 (pp) REVERT: H 102 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8412 (tttp) REVERT: H 113 ASP cc_start: 0.7528 (m-30) cc_final: 0.7242 (m-30) REVERT: H 147 ASN cc_start: 0.8191 (m-40) cc_final: 0.7839 (m110) REVERT: H 210 ARG cc_start: 0.8451 (ptp90) cc_final: 0.8207 (ptp-110) REVERT: H 239 VAL cc_start: 0.8276 (p) cc_final: 0.8042 (t) REVERT: H 247 SER cc_start: 0.8331 (m) cc_final: 0.8064 (p) REVERT: H 356 ASP cc_start: 0.8106 (t0) cc_final: 0.7864 (t0) REVERT: H 389 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8558 (mttt) REVERT: J 45 ASN cc_start: 0.8361 (m-40) cc_final: 0.8079 (t0) REVERT: J 46 LEU cc_start: 0.8727 (tp) cc_final: 0.8472 (tp) REVERT: J 77 SER cc_start: 0.8400 (t) cc_final: 0.7867 (p) outliers start: 89 outliers final: 37 residues processed: 504 average time/residue: 1.1647 time to fit residues: 667.9034 Evaluate side-chains 481 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 433 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 0.1980 chunk 126 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 147 ASN A 199 ASN A 226 GLN A 465 ASN N 89 GLN B 93 ASN B 199 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN E 93 ASN E 136 GLN E 199 ASN E 226 GLN E 441 ASN H 136 GLN H 226 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.092171 restraints weight = 28162.621| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.87 r_work: 0.2990 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20024 Z= 0.125 Angle : 0.570 6.458 27232 Z= 0.299 Chirality : 0.044 0.133 2952 Planarity : 0.004 0.047 3476 Dihedral : 5.010 20.718 3048 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.85 % Favored : 93.98 % Rotamer: Outliers : 3.77 % Allowed : 15.19 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 2460 helix: -0.70 (0.92), residues: 24 sheet: 0.12 (0.18), residues: 848 loop : -2.59 (0.12), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 178 HIS 0.002 0.001 HIS A 184 PHE 0.016 0.002 PHE E 410 TYR 0.015 0.001 TYR N 94 ARG 0.003 0.000 ARG B 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 16) link_NAG-ASN : angle 2.24093 ( 48) hydrogen bonds : bond 0.03718 ( 552) hydrogen bonds : angle 5.59374 ( 1620) SS BOND : bond 0.00178 ( 36) SS BOND : angle 0.90935 ( 72) covalent geometry : bond 0.00290 (19972) covalent geometry : angle 0.56102 (27112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 439 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 VAL cc_start: 0.8248 (p) cc_final: 0.8041 (t) REVERT: A 247 SER cc_start: 0.8415 (m) cc_final: 0.8186 (p) REVERT: A 389 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8510 (mttt) REVERT: A 435 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8441 (mtmt) REVERT: M 28 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7790 (ttmm) REVERT: M 37 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7994 (t) REVERT: N 92 ASP cc_start: 0.8359 (t0) cc_final: 0.7904 (t0) REVERT: N 95 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7551 (pp) REVERT: B 119 GLU cc_start: 0.7892 (mp0) cc_final: 0.7458 (mp0) REVERT: B 147 ASN cc_start: 0.7998 (m-40) cc_final: 0.7694 (m110) REVERT: B 247 SER cc_start: 0.8360 (m) cc_final: 0.8093 (p) REVERT: B 362 MET cc_start: 0.8536 (ptm) cc_final: 0.8046 (ptp) REVERT: B 391 GLN cc_start: 0.8395 (pt0) cc_final: 0.8114 (pt0) REVERT: B 393 ASN cc_start: 0.8510 (m110) cc_final: 0.8179 (m-40) REVERT: D 46 LEU cc_start: 0.8685 (tp) cc_final: 0.8397 (tp) REVERT: D 77 SER cc_start: 0.8016 (t) cc_final: 0.7805 (t) REVERT: D 92 ASP cc_start: 0.8340 (t0) cc_final: 0.7836 (t0) REVERT: D 93 SER cc_start: 0.8112 (p) cc_final: 0.7792 (p) REVERT: D 95 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7367 (pp) REVERT: E 147 ASN cc_start: 0.8088 (m-40) cc_final: 0.7760 (m110) REVERT: E 210 ARG cc_start: 0.8340 (ptp90) cc_final: 0.8085 (ptp-110) REVERT: E 213 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: E 332 VAL cc_start: 0.8589 (t) cc_final: 0.8360 (m) REVERT: E 392 THR cc_start: 0.8281 (t) cc_final: 0.7972 (m) REVERT: F 28 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7663 (ttmm) REVERT: F 100 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7790 (ttp-170) REVERT: G 95 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7788 (pp) REVERT: H 113 ASP cc_start: 0.7502 (m-30) cc_final: 0.7240 (m-30) REVERT: H 147 ASN cc_start: 0.8152 (m-40) cc_final: 0.7797 (m110) REVERT: H 210 ARG cc_start: 0.8390 (ptp90) cc_final: 0.8109 (ptp-110) REVERT: H 247 SER cc_start: 0.8294 (m) cc_final: 0.8037 (p) REVERT: I 28 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7808 (ttmm) REVERT: J 45 ASN cc_start: 0.8344 (m-40) cc_final: 0.8067 (t0) REVERT: J 46 LEU cc_start: 0.8708 (tp) cc_final: 0.8443 (tp) REVERT: J 77 SER cc_start: 0.8421 (t) cc_final: 0.7873 (p) REVERT: J 89 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8084 (tm-30) outliers start: 80 outliers final: 41 residues processed: 485 average time/residue: 1.1309 time to fit residues: 628.0186 Evaluate side-chains 463 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 411 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 226 GLN B 93 ASN B 199 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN E 93 ASN E 136 GLN E 199 ASN E 226 GLN E 393 ASN G 45 ASN G 89 GLN H 226 GLN ** H 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092216 restraints weight = 28618.931| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.91 r_work: 0.2977 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20024 Z= 0.112 Angle : 0.552 6.420 27232 Z= 0.289 Chirality : 0.044 0.145 2952 Planarity : 0.004 0.046 3476 Dihedral : 4.803 20.646 3048 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 4.43 % Allowed : 15.38 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 2460 helix: -0.16 (1.01), residues: 24 sheet: 0.30 (0.18), residues: 844 loop : -2.49 (0.12), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 178 HIS 0.002 0.001 HIS H 144 PHE 0.015 0.002 PHE E 410 TYR 0.019 0.001 TYR N 94 ARG 0.003 0.000 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 16) link_NAG-ASN : angle 2.10466 ( 48) hydrogen bonds : bond 0.03530 ( 552) hydrogen bonds : angle 5.43809 ( 1620) SS BOND : bond 0.00213 ( 36) SS BOND : angle 1.07938 ( 72) covalent geometry : bond 0.00258 (19972) covalent geometry : angle 0.54366 (27112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 426 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7979 (m110) cc_final: 0.7678 (m110) REVERT: A 239 VAL cc_start: 0.8243 (p) cc_final: 0.8041 (t) REVERT: A 247 SER cc_start: 0.8417 (m) cc_final: 0.8169 (p) REVERT: A 389 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8520 (mttt) REVERT: A 392 THR cc_start: 0.8435 (m) cc_final: 0.8026 (t) REVERT: A 431 LYS cc_start: 0.7821 (tppt) cc_final: 0.7476 (tppt) REVERT: A 443 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8023 (tt) REVERT: M 28 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7785 (ttmm) REVERT: M 37 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7978 (t) REVERT: N 92 ASP cc_start: 0.8397 (t0) cc_final: 0.7943 (t0) REVERT: N 95 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7583 (pp) REVERT: B 119 GLU cc_start: 0.7922 (mp0) cc_final: 0.7493 (mp0) REVERT: B 147 ASN cc_start: 0.8006 (m-40) cc_final: 0.7696 (m110) REVERT: B 247 SER cc_start: 0.8386 (m) cc_final: 0.8123 (p) REVERT: B 362 MET cc_start: 0.8524 (ptm) cc_final: 0.8005 (ptp) REVERT: B 369 THR cc_start: 0.8644 (p) cc_final: 0.8412 (p) REVERT: B 391 GLN cc_start: 0.8358 (pt0) cc_final: 0.8081 (pt0) REVERT: B 393 ASN cc_start: 0.8488 (m110) cc_final: 0.8188 (m-40) REVERT: D 46 LEU cc_start: 0.8700 (tp) cc_final: 0.8316 (tp) REVERT: D 77 SER cc_start: 0.8025 (t) cc_final: 0.7815 (t) REVERT: D 92 ASP cc_start: 0.8383 (t0) cc_final: 0.7872 (t0) REVERT: D 93 SER cc_start: 0.8128 (p) cc_final: 0.7900 (p) REVERT: D 95 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7419 (pp) REVERT: E 147 ASN cc_start: 0.8080 (m-40) cc_final: 0.7753 (m110) REVERT: E 210 ARG cc_start: 0.8338 (ptp90) cc_final: 0.8082 (ptp-110) REVERT: E 213 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: G 77 SER cc_start: 0.8542 (t) cc_final: 0.8067 (p) REVERT: G 92 ASP cc_start: 0.8340 (t0) cc_final: 0.7899 (t0) REVERT: G 95 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7885 (pp) REVERT: H 113 ASP cc_start: 0.7527 (m-30) cc_final: 0.7257 (m-30) REVERT: H 147 ASN cc_start: 0.8122 (m-40) cc_final: 0.7763 (m110) REVERT: H 210 ARG cc_start: 0.8401 (ptp90) cc_final: 0.8130 (ptp-110) REVERT: H 247 SER cc_start: 0.8295 (m) cc_final: 0.8057 (p) REVERT: H 389 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8587 (mttt) REVERT: I 28 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7787 (ttmm) REVERT: J 45 ASN cc_start: 0.8354 (m-40) cc_final: 0.8108 (t0) REVERT: J 46 LEU cc_start: 0.8705 (tp) cc_final: 0.8428 (tp) REVERT: J 77 SER cc_start: 0.8471 (t) cc_final: 0.7944 (p) REVERT: J 89 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: J 92 ASP cc_start: 0.8445 (t0) cc_final: 0.7980 (t0) outliers start: 94 outliers final: 46 residues processed: 478 average time/residue: 1.1328 time to fit residues: 617.8107 Evaluate side-chains 477 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 420 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 93 ASN A 136 GLN A 226 GLN B 93 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 136 GLN E 199 ASN E 226 GLN G 45 ASN H 226 GLN ** H 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.093199 restraints weight = 28454.079| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.93 r_work: 0.2952 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20024 Z= 0.148 Angle : 0.580 6.361 27232 Z= 0.305 Chirality : 0.045 0.152 2952 Planarity : 0.004 0.047 3476 Dihedral : 4.944 20.318 3048 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.98 % Favored : 93.86 % Rotamer: Outliers : 4.67 % Allowed : 15.09 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2460 helix: -0.08 (1.04), residues: 24 sheet: 0.35 (0.18), residues: 888 loop : -2.46 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 178 HIS 0.003 0.001 HIS H 144 PHE 0.017 0.002 PHE E 410 TYR 0.022 0.002 TYR N 94 ARG 0.003 0.000 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 16) link_NAG-ASN : angle 2.22377 ( 48) hydrogen bonds : bond 0.03881 ( 552) hydrogen bonds : angle 5.52417 ( 1620) SS BOND : bond 0.00200 ( 36) SS BOND : angle 1.36378 ( 72) covalent geometry : bond 0.00352 (19972) covalent geometry : angle 0.56898 (27112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 428 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7994 (m110) cc_final: 0.7685 (m110) REVERT: A 247 SER cc_start: 0.8395 (m) cc_final: 0.8160 (p) REVERT: A 389 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8510 (mttt) REVERT: A 431 LYS cc_start: 0.7854 (tppt) cc_final: 0.7514 (tppt) REVERT: A 443 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.8000 (tt) REVERT: M 87 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7552 (p) REVERT: N 92 ASP cc_start: 0.8441 (t0) cc_final: 0.8016 (t0) REVERT: N 95 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7591 (pp) REVERT: B 119 GLU cc_start: 0.7958 (mp0) cc_final: 0.7500 (mp0) REVERT: B 147 ASN cc_start: 0.8010 (m-40) cc_final: 0.7717 (m110) REVERT: B 213 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: B 247 SER cc_start: 0.8378 (m) cc_final: 0.8102 (p) REVERT: B 391 GLN cc_start: 0.8356 (pt0) cc_final: 0.8047 (pt0) REVERT: B 393 ASN cc_start: 0.8487 (m110) cc_final: 0.8194 (m-40) REVERT: C 28 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7618 (ttmm) REVERT: C 78 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8125 (tt) REVERT: C 87 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7511 (p) REVERT: C 100 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7893 (ttp-170) REVERT: C 102 LEU cc_start: 0.8270 (pp) cc_final: 0.8048 (pt) REVERT: D 46 LEU cc_start: 0.8654 (tp) cc_final: 0.8321 (tp) REVERT: D 61 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.6555 (ptt90) REVERT: D 77 SER cc_start: 0.8078 (t) cc_final: 0.7693 (t) REVERT: D 92 ASP cc_start: 0.8420 (t0) cc_final: 0.7919 (t0) REVERT: D 93 SER cc_start: 0.8098 (p) cc_final: 0.7809 (p) REVERT: D 95 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7505 (pp) REVERT: E 147 ASN cc_start: 0.8122 (m-40) cc_final: 0.7788 (m110) REVERT: E 210 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8090 (ptp-110) REVERT: E 213 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: E 389 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8327 (mttm) REVERT: E 431 LYS cc_start: 0.7822 (tppt) cc_final: 0.7496 (tppt) REVERT: G 77 SER cc_start: 0.8554 (t) cc_final: 0.8089 (p) REVERT: G 92 ASP cc_start: 0.8433 (t0) cc_final: 0.8034 (t0) REVERT: H 113 ASP cc_start: 0.7580 (m-30) cc_final: 0.7256 (m-30) REVERT: H 147 ASN cc_start: 0.8122 (m-40) cc_final: 0.7768 (m110) REVERT: H 210 ARG cc_start: 0.8435 (ptp90) cc_final: 0.8158 (ptp-110) REVERT: H 247 SER cc_start: 0.8290 (m) cc_final: 0.8039 (p) REVERT: H 392 THR cc_start: 0.8479 (m) cc_final: 0.8125 (t) REVERT: I 28 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7726 (ttpp) REVERT: I 63 VAL cc_start: 0.8621 (m) cc_final: 0.8389 (t) REVERT: J 45 ASN cc_start: 0.8369 (m-40) cc_final: 0.8101 (t0) REVERT: J 46 LEU cc_start: 0.8731 (tp) cc_final: 0.8422 (tp) REVERT: J 61 ARG cc_start: 0.8390 (ptp90) cc_final: 0.8001 (ptp90) REVERT: J 77 SER cc_start: 0.8413 (t) cc_final: 0.7886 (p) REVERT: J 89 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: J 92 ASP cc_start: 0.8485 (t0) cc_final: 0.8022 (t0) outliers start: 99 outliers final: 55 residues processed: 481 average time/residue: 1.1256 time to fit residues: 617.4483 Evaluate side-chains 484 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 414 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain H residue 311 SER Chi-restraints excluded: chain H residue 417 CYS Chi-restraints excluded: chain H residue 443 ILE Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 95 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 0.0970 chunk 133 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 226 GLN A 294 ASN B 294 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 136 GLN E 184 HIS E 199 ASN E 226 GLN G 45 ASN H 226 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092154 restraints weight = 28344.608| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.90 r_work: 0.2998 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20024 Z= 0.106 Angle : 0.540 6.274 27232 Z= 0.283 Chirality : 0.044 0.146 2952 Planarity : 0.004 0.047 3476 Dihedral : 4.697 20.251 3048 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 4.39 % Allowed : 15.99 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2460 helix: 0.25 (1.07), residues: 24 sheet: 0.53 (0.18), residues: 892 loop : -2.36 (0.13), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 178 HIS 0.003 0.001 HIS H 144 PHE 0.014 0.001 PHE A 410 TYR 0.023 0.001 TYR N 94 ARG 0.003 0.000 ARG N 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 16) link_NAG-ASN : angle 1.99646 ( 48) hydrogen bonds : bond 0.03391 ( 552) hydrogen bonds : angle 5.35533 ( 1620) SS BOND : bond 0.00182 ( 36) SS BOND : angle 1.13021 ( 72) covalent geometry : bond 0.00244 (19972) covalent geometry : angle 0.53182 (27112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 425 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.6869 (ttt180) REVERT: A 147 ASN cc_start: 0.7967 (m110) cc_final: 0.7670 (m110) REVERT: A 222 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7141 (mm) REVERT: A 247 SER cc_start: 0.8381 (m) cc_final: 0.8149 (p) REVERT: A 389 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8515 (mttt) REVERT: A 391 GLN cc_start: 0.7776 (pt0) cc_final: 0.7458 (pt0) REVERT: A 431 LYS cc_start: 0.7797 (tppt) cc_final: 0.7457 (tppt) REVERT: N 92 ASP cc_start: 0.8398 (t0) cc_final: 0.7957 (t0) REVERT: N 95 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7536 (pp) REVERT: B 119 GLU cc_start: 0.7977 (mp0) cc_final: 0.7539 (mp0) REVERT: B 147 ASN cc_start: 0.7991 (m-40) cc_final: 0.7692 (m110) REVERT: B 213 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: B 247 SER cc_start: 0.8386 (m) cc_final: 0.8117 (p) REVERT: B 362 MET cc_start: 0.8424 (ptp) cc_final: 0.7997 (ptp) REVERT: B 369 THR cc_start: 0.8654 (p) cc_final: 0.8388 (p) REVERT: B 391 GLN cc_start: 0.8330 (pt0) cc_final: 0.8023 (pt0) REVERT: B 393 ASN cc_start: 0.8482 (m110) cc_final: 0.8200 (m-40) REVERT: C 28 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7546 (ttmm) REVERT: C 87 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7454 (p) REVERT: C 100 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7952 (ttp-170) REVERT: C 102 LEU cc_start: 0.8246 (pp) cc_final: 0.8020 (pt) REVERT: D 46 LEU cc_start: 0.8618 (tp) cc_final: 0.8297 (tp) REVERT: D 92 ASP cc_start: 0.8374 (t0) cc_final: 0.7879 (t0) REVERT: D 93 SER cc_start: 0.8124 (p) cc_final: 0.7892 (p) REVERT: D 95 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7435 (pp) REVERT: E 147 ASN cc_start: 0.8091 (m-40) cc_final: 0.7767 (m110) REVERT: E 210 ARG cc_start: 0.8352 (ptp90) cc_final: 0.8093 (ptp-110) REVERT: E 213 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: E 431 LYS cc_start: 0.7780 (tppt) cc_final: 0.7447 (tppt) REVERT: F 87 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7490 (p) REVERT: G 61 ARG cc_start: 0.8252 (ptp90) cc_final: 0.7881 (ptp90) REVERT: G 77 SER cc_start: 0.8533 (t) cc_final: 0.8055 (p) REVERT: G 92 ASP cc_start: 0.8387 (t0) cc_final: 0.7965 (t0) REVERT: H 113 ASP cc_start: 0.7571 (m-30) cc_final: 0.7281 (m-30) REVERT: H 147 ASN cc_start: 0.8117 (m-40) cc_final: 0.7765 (m110) REVERT: H 210 ARG cc_start: 0.8426 (ptp90) cc_final: 0.8148 (ptp-110) REVERT: H 247 SER cc_start: 0.8309 (m) cc_final: 0.8071 (p) REVERT: H 391 GLN cc_start: 0.7839 (pt0) cc_final: 0.7489 (pt0) REVERT: H 392 THR cc_start: 0.8481 (m) cc_final: 0.8104 (t) REVERT: H 431 LYS cc_start: 0.7775 (tppt) cc_final: 0.7431 (tppt) REVERT: I 63 VAL cc_start: 0.8616 (m) cc_final: 0.8402 (t) REVERT: J 45 ASN cc_start: 0.8320 (m-40) cc_final: 0.8058 (t0) REVERT: J 46 LEU cc_start: 0.8709 (tp) cc_final: 0.8406 (tp) REVERT: J 61 ARG cc_start: 0.8382 (ptp90) cc_final: 0.8002 (ptp90) REVERT: J 77 SER cc_start: 0.8403 (t) cc_final: 0.7847 (p) REVERT: J 89 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: J 92 ASP cc_start: 0.8437 (t0) cc_final: 0.7967 (t0) outliers start: 93 outliers final: 51 residues processed: 475 average time/residue: 1.1635 time to fit residues: 643.7779 Evaluate side-chains 493 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 430 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 226 GLN Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 417 CYS Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 227 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 226 GLN N 89 GLN B 86 ASN B 93 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN E 226 GLN H 226 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093189 restraints weight = 28339.202| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.93 r_work: 0.2965 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20024 Z= 0.142 Angle : 0.576 6.279 27232 Z= 0.302 Chirality : 0.045 0.168 2952 Planarity : 0.004 0.048 3476 Dihedral : 4.852 20.147 3048 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.77 % Favored : 94.07 % Rotamer: Outliers : 3.68 % Allowed : 16.93 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.16), residues: 2460 helix: 0.10 (1.05), residues: 24 sheet: 0.51 (0.18), residues: 888 loop : -2.35 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 178 HIS 0.004 0.001 HIS E 184 PHE 0.017 0.002 PHE E 410 TYR 0.027 0.002 TYR N 94 ARG 0.004 0.000 ARG N 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 2.15336 ( 48) hydrogen bonds : bond 0.03766 ( 552) hydrogen bonds : angle 5.44107 ( 1620) SS BOND : bond 0.00216 ( 36) SS BOND : angle 1.32001 ( 72) covalent geometry : bond 0.00337 (19972) covalent geometry : angle 0.56560 (27112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 427 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8010 (m110) cc_final: 0.7721 (m110) REVERT: A 247 SER cc_start: 0.8410 (m) cc_final: 0.8174 (p) REVERT: A 389 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8512 (mttt) REVERT: A 391 GLN cc_start: 0.7803 (pt0) cc_final: 0.7484 (pt0) REVERT: A 431 LYS cc_start: 0.7839 (tppt) cc_final: 0.7477 (tppt) REVERT: A 435 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8401 (mtmt) REVERT: N 92 ASP cc_start: 0.8462 (t0) cc_final: 0.8036 (t0) REVERT: N 95 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7603 (pp) REVERT: B 119 GLU cc_start: 0.7976 (mp0) cc_final: 0.7549 (mp0) REVERT: B 147 ASN cc_start: 0.8020 (m-40) cc_final: 0.7724 (m110) REVERT: B 213 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: B 247 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 362 MET cc_start: 0.8449 (ptp) cc_final: 0.8034 (ptp) REVERT: B 391 GLN cc_start: 0.8330 (pt0) cc_final: 0.8011 (pt0) REVERT: B 393 ASN cc_start: 0.8484 (m110) cc_final: 0.8210 (m-40) REVERT: C 28 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7587 (ttmm) REVERT: C 100 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7975 (ttp-170) REVERT: D 46 LEU cc_start: 0.8659 (tp) cc_final: 0.8306 (tp) REVERT: D 92 ASP cc_start: 0.8428 (t0) cc_final: 0.7962 (t0) REVERT: D 93 SER cc_start: 0.8121 (p) cc_final: 0.7889 (p) REVERT: D 95 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7494 (pp) REVERT: E 147 ASN cc_start: 0.8120 (m-40) cc_final: 0.7811 (m110) REVERT: E 210 ARG cc_start: 0.8354 (ptp90) cc_final: 0.8090 (ptp-110) REVERT: E 213 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: E 356 ASP cc_start: 0.8027 (t0) cc_final: 0.7822 (OUTLIER) REVERT: E 431 LYS cc_start: 0.7820 (tppt) cc_final: 0.7481 (tppt) REVERT: F 87 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7583 (p) REVERT: G 61 ARG cc_start: 0.8265 (ptp90) cc_final: 0.7905 (ptp90) REVERT: G 77 SER cc_start: 0.8523 (t) cc_final: 0.8012 (p) REVERT: G 92 ASP cc_start: 0.8436 (t0) cc_final: 0.8017 (t0) REVERT: H 113 ASP cc_start: 0.7595 (m-30) cc_final: 0.7265 (m-30) REVERT: H 147 ASN cc_start: 0.8114 (m-40) cc_final: 0.7759 (m110) REVERT: H 210 ARG cc_start: 0.8434 (ptp90) cc_final: 0.8142 (ptp-110) REVERT: H 247 SER cc_start: 0.8308 (m) cc_final: 0.8052 (p) REVERT: H 392 THR cc_start: 0.8489 (m) cc_final: 0.8125 (t) REVERT: H 431 LYS cc_start: 0.7832 (tppt) cc_final: 0.7475 (tppt) REVERT: I 63 VAL cc_start: 0.8630 (m) cc_final: 0.8386 (t) REVERT: J 45 ASN cc_start: 0.8366 (m-40) cc_final: 0.8108 (t0) REVERT: J 46 LEU cc_start: 0.8733 (tp) cc_final: 0.8425 (tp) REVERT: J 77 SER cc_start: 0.8358 (t) cc_final: 0.7824 (p) REVERT: J 89 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: J 92 ASP cc_start: 0.8499 (t0) cc_final: 0.8084 (t0) outliers start: 78 outliers final: 55 residues processed: 462 average time/residue: 1.0874 time to fit residues: 574.2444 Evaluate side-chains 480 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 416 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 417 CYS Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 0.3980 chunk 229 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 226 GLN E 136 GLN E 226 GLN H 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093512 restraints weight = 28428.561| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.93 r_work: 0.2966 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20024 Z= 0.130 Angle : 0.566 6.486 27232 Z= 0.296 Chirality : 0.045 0.164 2952 Planarity : 0.004 0.047 3476 Dihedral : 4.796 20.098 3048 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 3.49 % Allowed : 17.17 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2460 helix: 0.20 (1.06), residues: 24 sheet: 0.55 (0.18), residues: 888 loop : -2.31 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 178 HIS 0.003 0.001 HIS E 184 PHE 0.016 0.002 PHE E 410 TYR 0.026 0.001 TYR N 94 ARG 0.004 0.000 ARG N 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 16) link_NAG-ASN : angle 2.06310 ( 48) hydrogen bonds : bond 0.03617 ( 552) hydrogen bonds : angle 5.39699 ( 1620) SS BOND : bond 0.00215 ( 36) SS BOND : angle 1.20443 ( 72) covalent geometry : bond 0.00307 (19972) covalent geometry : angle 0.55743 (27112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 433 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8012 (m110) cc_final: 0.7727 (m110) REVERT: A 222 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7261 (mm) REVERT: A 247 SER cc_start: 0.8395 (m) cc_final: 0.8161 (p) REVERT: A 389 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8507 (mttt) REVERT: A 391 GLN cc_start: 0.7793 (pt0) cc_final: 0.7470 (pt0) REVERT: A 416 SER cc_start: 0.8565 (m) cc_final: 0.8326 (t) REVERT: A 431 LYS cc_start: 0.7845 (tppt) cc_final: 0.7491 (tppt) REVERT: N 45 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8066 (t0) REVERT: N 77 SER cc_start: 0.8237 (t) cc_final: 0.7676 (p) REVERT: N 92 ASP cc_start: 0.8455 (t0) cc_final: 0.8033 (t0) REVERT: N 95 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7551 (pp) REVERT: B 119 GLU cc_start: 0.7988 (mp0) cc_final: 0.7583 (mp0) REVERT: B 147 ASN cc_start: 0.8015 (m-40) cc_final: 0.7722 (m110) REVERT: B 213 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: B 247 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8148 (p) REVERT: B 362 MET cc_start: 0.8427 (ptp) cc_final: 0.8014 (ptp) REVERT: B 369 THR cc_start: 0.8655 (p) cc_final: 0.8403 (p) REVERT: B 391 GLN cc_start: 0.8318 (pt0) cc_final: 0.8009 (pt0) REVERT: B 393 ASN cc_start: 0.8482 (m110) cc_final: 0.8217 (m-40) REVERT: B 442 SER cc_start: 0.8249 (p) cc_final: 0.8018 (t) REVERT: C 28 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7577 (ttmm) REVERT: C 100 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: D 46 LEU cc_start: 0.8656 (tp) cc_final: 0.8309 (tp) REVERT: D 92 ASP cc_start: 0.8428 (t0) cc_final: 0.7950 (t0) REVERT: D 93 SER cc_start: 0.8120 (p) cc_final: 0.7887 (p) REVERT: D 95 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7487 (pp) REVERT: E 147 ASN cc_start: 0.8123 (m-40) cc_final: 0.7813 (m110) REVERT: E 210 ARG cc_start: 0.8354 (ptp90) cc_final: 0.8089 (ptp-110) REVERT: E 213 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: E 356 ASP cc_start: 0.8033 (t0) cc_final: 0.7832 (OUTLIER) REVERT: E 431 LYS cc_start: 0.7816 (tppt) cc_final: 0.7468 (tppt) REVERT: E 465 ASN cc_start: 0.8313 (p0) cc_final: 0.8111 (p0) REVERT: F 87 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7545 (p) REVERT: G 61 ARG cc_start: 0.8233 (ptp90) cc_final: 0.7843 (ptp90) REVERT: G 77 SER cc_start: 0.8509 (t) cc_final: 0.7979 (p) REVERT: G 92 ASP cc_start: 0.8420 (t0) cc_final: 0.8014 (t0) REVERT: H 113 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: H 147 ASN cc_start: 0.8121 (m-40) cc_final: 0.7738 (m110) REVERT: H 210 ARG cc_start: 0.8431 (ptp90) cc_final: 0.8139 (ptp-110) REVERT: H 222 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7145 (mm) REVERT: H 247 SER cc_start: 0.8311 (m) cc_final: 0.8057 (p) REVERT: H 392 THR cc_start: 0.8492 (m) cc_final: 0.8137 (t) REVERT: H 431 LYS cc_start: 0.7834 (tppt) cc_final: 0.7477 (tppt) REVERT: H 465 ASN cc_start: 0.8315 (p0) cc_final: 0.8071 (p0) REVERT: I 63 VAL cc_start: 0.8630 (m) cc_final: 0.8395 (t) REVERT: J 45 ASN cc_start: 0.8367 (m-40) cc_final: 0.8107 (t0) REVERT: J 46 LEU cc_start: 0.8729 (tp) cc_final: 0.8423 (tp) REVERT: J 61 ARG cc_start: 0.8284 (ptp90) cc_final: 0.7950 (ptp90) REVERT: J 77 SER cc_start: 0.8401 (t) cc_final: 0.7822 (p) REVERT: J 89 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: J 92 ASP cc_start: 0.8494 (t0) cc_final: 0.8080 (t0) outliers start: 74 outliers final: 56 residues processed: 466 average time/residue: 1.0575 time to fit residues: 566.0458 Evaluate side-chains 498 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 429 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 45 ASN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 417 CYS Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 226 GLN N 27 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 136 GLN E 226 GLN H 226 GLN J 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090973 restraints weight = 28309.648| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.92 r_work: 0.2926 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20024 Z= 0.253 Angle : 0.676 6.992 27232 Z= 0.357 Chirality : 0.049 0.186 2952 Planarity : 0.005 0.052 3476 Dihedral : 5.344 22.046 3048 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.75 % Favored : 93.09 % Rotamer: Outliers : 3.58 % Allowed : 17.50 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2460 helix: -0.28 (1.01), residues: 24 sheet: 0.43 (0.18), residues: 888 loop : -2.44 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 178 HIS 0.005 0.001 HIS E 184 PHE 0.021 0.003 PHE E 410 TYR 0.034 0.002 TYR N 94 ARG 0.006 0.001 ARG C 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 16) link_NAG-ASN : angle 2.52147 ( 48) hydrogen bonds : bond 0.04700 ( 552) hydrogen bonds : angle 5.73220 ( 1620) SS BOND : bond 0.00246 ( 36) SS BOND : angle 1.60436 ( 72) covalent geometry : bond 0.00612 (19972) covalent geometry : angle 0.66400 (27112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 440 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8018 (m110) cc_final: 0.7718 (m110) REVERT: A 247 SER cc_start: 0.8448 (m) cc_final: 0.8205 (p) REVERT: A 389 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8570 (mttt) REVERT: A 391 GLN cc_start: 0.7875 (pt0) cc_final: 0.7519 (pt0) REVERT: A 431 LYS cc_start: 0.7870 (tppt) cc_final: 0.7512 (tppt) REVERT: N 45 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8094 (t0) REVERT: N 77 SER cc_start: 0.8292 (t) cc_final: 0.7788 (p) REVERT: N 92 ASP cc_start: 0.8530 (t0) cc_final: 0.8096 (t0) REVERT: N 95 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7597 (pp) REVERT: B 119 GLU cc_start: 0.8018 (mp0) cc_final: 0.7582 (mp0) REVERT: B 147 ASN cc_start: 0.8051 (m-40) cc_final: 0.7748 (m110) REVERT: B 213 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: B 247 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 393 ASN cc_start: 0.8497 (m110) cc_final: 0.8202 (m-40) REVERT: C 28 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7655 (ttmm) REVERT: C 100 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.7960 (ttp-170) REVERT: D 92 ASP cc_start: 0.8390 (t0) cc_final: 0.7947 (t0) REVERT: D 93 SER cc_start: 0.8136 (p) cc_final: 0.7839 (p) REVERT: D 95 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7516 (pp) REVERT: E 147 ASN cc_start: 0.8169 (m-40) cc_final: 0.7833 (m110) REVERT: E 210 ARG cc_start: 0.8382 (ptp90) cc_final: 0.8068 (ptp-110) REVERT: E 213 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: E 356 ASP cc_start: 0.8042 (t0) cc_final: 0.7841 (t0) REVERT: E 431 LYS cc_start: 0.7856 (tppt) cc_final: 0.7503 (tppt) REVERT: F 87 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7667 (p) REVERT: G 77 SER cc_start: 0.8525 (t) cc_final: 0.8011 (p) REVERT: G 92 ASP cc_start: 0.8428 (t0) cc_final: 0.8031 (t0) REVERT: H 113 ASP cc_start: 0.7633 (m-30) cc_final: 0.7426 (m-30) REVERT: H 147 ASN cc_start: 0.8172 (m-40) cc_final: 0.7813 (m110) REVERT: H 210 ARG cc_start: 0.8471 (ptp90) cc_final: 0.8180 (ptp-110) REVERT: H 247 SER cc_start: 0.8347 (m) cc_final: 0.8088 (p) REVERT: H 392 THR cc_start: 0.8528 (m) cc_final: 0.8171 (t) REVERT: J 45 ASN cc_start: 0.8406 (m-40) cc_final: 0.8116 (t0) REVERT: J 46 LEU cc_start: 0.8771 (tp) cc_final: 0.8448 (tp) REVERT: J 61 ARG cc_start: 0.8281 (ptp90) cc_final: 0.7867 (ptp90) REVERT: J 77 SER cc_start: 0.8392 (t) cc_final: 0.7867 (p) REVERT: J 89 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: J 92 ASP cc_start: 0.8532 (t0) cc_final: 0.8112 (t0) outliers start: 76 outliers final: 51 residues processed: 473 average time/residue: 1.0807 time to fit residues: 584.9059 Evaluate side-chains 496 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 434 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 45 ASN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 417 CYS Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 229 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 225 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 232 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 199 ASN A 226 GLN B 199 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 136 GLN E 199 ASN E 226 GLN G 89 GLN H 226 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093335 restraints weight = 28285.502| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.93 r_work: 0.2967 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20024 Z= 0.122 Angle : 0.573 7.690 27232 Z= 0.299 Chirality : 0.045 0.281 2952 Planarity : 0.004 0.050 3476 Dihedral : 4.831 20.089 3048 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.85 % Favored : 93.98 % Rotamer: Outliers : 3.30 % Allowed : 18.30 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2460 helix: 0.22 (1.08), residues: 24 sheet: 0.49 (0.18), residues: 908 loop : -2.33 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 178 HIS 0.004 0.001 HIS H 144 PHE 0.016 0.002 PHE A 410 TYR 0.028 0.001 TYR N 94 ARG 0.004 0.000 ARG N 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 16) link_NAG-ASN : angle 1.97423 ( 48) hydrogen bonds : bond 0.03530 ( 552) hydrogen bonds : angle 5.40510 ( 1620) SS BOND : bond 0.00192 ( 36) SS BOND : angle 1.26640 ( 72) covalent geometry : bond 0.00286 (19972) covalent geometry : angle 0.56483 (27112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14402.24 seconds wall clock time: 248 minutes 16.74 seconds (14896.74 seconds total)