Starting phenix.real_space_refine on Sun Aug 24 11:15:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gat_29907/08_2025/8gat_29907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gat_29907/08_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_29907/08_2025/8gat_29907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gat_29907/08_2025/8gat_29907.map" model { file = "/net/cci-nas-00/data/ceres_data/8gat_29907/08_2025/8gat_29907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gat_29907/08_2025/8gat_29907.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: "M" 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: "N" 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} 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 Restraints were copied for chains: B, E, H, C, F, I, D, G, J Time building chain proxies: 2.85, per 1000 atoms: 0.15 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=44, 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 M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 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: 1.44 Conformation dependent library (CDL) restraints added in 623.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.71 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: 3.43 Time building geometry restraints manager: 1.98 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: 11540 20.34 - 40.67: 308 40.67 - 61.01: 84 61.01 - 81.34: 12 81.34 - 101.68: 32 Dihedral angle restraints: 11976 sinusoidal: 4932 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 11973 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: 72 2.51 - 3.11: 12528 3.11 - 3.70: 27132 3.70 - 4.30: 40240 4.30 - 4.90: 71028 Nonbonded interactions: 151000 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=" O ASN C 52 " pdb=" NH2 ARG C 71 " model vdw 2.114 3.120 ... (remaining 150995 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'N' selection = chain 'D' selection = chain 'G' selection = chain 'J' } 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: 1.900 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- 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 20032 Z= 0.281 Angle : 0.992 12.384 27248 Z= 0.551 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG J 61 TYR 0.025 0.003 TYR B 406 PHE 0.025 0.004 PHE B 410 TRP 0.046 0.004 TRP M 52A HIS 0.007 0.002 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00599 (19972) covalent geometry : angle 0.97982 (27112) SS BOND : bond 0.00447 ( 44) SS BOND : angle 1.79448 ( 88) hydrogen bonds : bond 0.27894 ( 552) hydrogen bonds : angle 9.73451 ( 1620) link_NAG-ASN : bond 0.00339 ( 16) link_NAG-ASN : angle 3.26198 ( 48) *********************** 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 : 0.475 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: 0.8009 (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: 0.7738 (t) REVERT: M 78 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7494 (tm) REVERT: M 91 TYR cc_start: 0.8073 (m-80) cc_final: 0.7828 (m-80) REVERT: N 46 LEU cc_start: 0.8614 (tp) cc_final: 0.8386 (tp) 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: 0.8368 (m-80) REVERT: C 78 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7399 (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: 0.7837 (p) REVERT: E 109 SER cc_start: 0.8268 (p) cc_final: 0.8063 (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: 0.8189 (m) REVERT: E 464 ILE cc_start: 0.8116 (pt) cc_final: 0.7832 (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: 0.7915 (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: 0.7505 (tm) REVERT: G 102 THR cc_start: 0.8183 (m) cc_final: 0.7847 (p) REVERT: H 109 SER cc_start: 0.8283 (p) cc_final: 0.8060 (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: 0.8141 (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: 0.7781 (t) REVERT: I 78 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7501 (tm) REVERT: I 91 TYR cc_start: 0.8095 (m-80) cc_final: 0.7815 (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: 0.4968 time to fit residues: 316.1850 Evaluate side-chains 480 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 467 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 M residue 78 LEU 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 216 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0000 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 N 55 GLN N 89 GLN B 147 ASN B 199 ASN B 226 GLN B 395 GLN D 55 GLN D 89 GLN E 93 ASN E 226 GLN E 395 GLN G 89 GLN H 226 GLN H 342 ASN H 393 ASN H 395 GLN J 89 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094410 restraints weight = 27626.678| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.87 r_work: 0.2996 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20032 Z= 0.129 Angle : 0.621 7.624 27248 Z= 0.325 Chirality : 0.045 0.174 2952 Planarity : 0.005 0.051 3476 Dihedral : 7.979 56.899 3082 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.14 % Favored : 93.70 % Rotamer: Outliers : 2.69 % Allowed : 11.37 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.14), residues: 2460 helix: -2.92 (0.63), residues: 24 sheet: -0.71 (0.17), residues: 884 loop : -2.94 (0.12), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.013 0.001 TYR J 49 PHE 0.021 0.002 PHE E 410 TRP 0.019 0.002 TRP H 295 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00289 (19972) covalent geometry : angle 0.61209 (27112) SS BOND : bond 0.00437 ( 44) SS BOND : angle 1.14794 ( 88) hydrogen bonds : bond 0.04183 ( 552) hydrogen bonds : angle 6.24683 ( 1620) link_NAG-ASN : bond 0.00204 ( 16) link_NAG-ASN : angle 2.24255 ( 48) *********************** 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 550 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 493 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8404 (p) cc_final: 0.8201 (p) REVERT: A 247 SER cc_start: 0.8367 (m) cc_final: 0.8100 (p) REVERT: A 356 ASP cc_start: 0.8136 (t0) cc_final: 0.7872 (t0) REVERT: A 392 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8221 (m) REVERT: A 431 LYS cc_start: 0.7987 (tppt) cc_final: 0.7630 (tppt) REVERT: A 457 SER cc_start: 0.8523 (t) cc_final: 0.8303 (m) REVERT: A 464 ILE cc_start: 0.8145 (pt) cc_final: 0.7793 (OUTLIER) REVERT: M 46 GLU cc_start: 0.8259 (tt0) cc_final: 0.8056 (tt0) REVERT: M 56 ILE cc_start: 0.8671 (mt) cc_final: 0.8380 (mt) REVERT: N 46 LEU cc_start: 0.8718 (tp) cc_final: 0.8495 (tp) REVERT: N 95 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7558 (pp) REVERT: B 147 ASN cc_start: 0.8011 (m-40) cc_final: 0.7781 (m110) REVERT: B 247 SER cc_start: 0.8302 (m) cc_final: 0.7996 (p) REVERT: B 249 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7832 (mtpp) REVERT: B 362 MET cc_start: 0.8562 (ptm) cc_final: 0.8094 (ptp) REVERT: B 393 ASN cc_start: 0.8546 (m110) cc_final: 0.8209 (m-40) REVERT: B 457 SER cc_start: 0.8555 (t) cc_final: 0.8348 (m) REVERT: B 464 ILE cc_start: 0.8182 (pt) cc_final: 0.7943 (OUTLIER) REVERT: C 28 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7541 (ttmm) REVERT: C 34 MET cc_start: 0.8617 (mmm) cc_final: 0.8398 (mmm) REVERT: C 46 GLU cc_start: 0.8224 (tt0) cc_final: 0.8018 (tt0) REVERT: C 78 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7741 (tm) REVERT: C 96 SER cc_start: 0.8713 (m) cc_final: 0.8497 (t) REVERT: D 46 LEU cc_start: 0.8661 (tp) cc_final: 0.8459 (tp) REVERT: D 87 TYR cc_start: 0.8340 (m-80) cc_final: 0.8096 (m-80) REVERT: D 92 ASP cc_start: 0.8275 (t0) cc_final: 0.7757 (t0) REVERT: D 93 SER cc_start: 0.8086 (p) cc_final: 0.7766 (p) REVERT: D 95 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7399 (pp) REVERT: E 147 ASN cc_start: 0.8058 (m-40) cc_final: 0.7738 (m-40) REVERT: E 210 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8081 (ptp-110) REVERT: E 393 ASN cc_start: 0.8468 (m110) cc_final: 0.8058 (m-40) REVERT: E 432 GLU cc_start: 0.7748 (mp0) cc_final: 0.7308 (mp0) REVERT: E 457 SER cc_start: 0.8500 (t) cc_final: 0.8283 (m) REVERT: E 464 ILE cc_start: 0.8178 (pt) cc_final: 0.7920 (OUTLIER) REVERT: F 28 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7659 (ttmm) REVERT: F 46 GLU cc_start: 0.8217 (tt0) cc_final: 0.8015 (tt0) REVERT: F 56 ILE cc_start: 0.8676 (mt) cc_final: 0.8399 (mt) REVERT: F 96 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8459 (t) REVERT: G 77 SER cc_start: 0.8106 (t) cc_final: 0.7506 (p) REVERT: G 87 TYR cc_start: 0.8314 (m-80) cc_final: 0.8016 (m-80) REVERT: G 95 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7790 (pp) REVERT: H 113 ASP cc_start: 0.7449 (m-30) cc_final: 0.7211 (m-30) REVERT: H 147 ASN cc_start: 0.8194 (m-40) cc_final: 0.7857 (m110) REVERT: H 210 ARG cc_start: 0.8421 (ptp90) cc_final: 0.8145 (ptp-110) REVERT: H 247 SER cc_start: 0.8273 (m) cc_final: 0.7991 (p) REVERT: H 457 SER cc_start: 0.8472 (t) cc_final: 0.8269 (m) REVERT: H 464 ILE cc_start: 0.8189 (pt) cc_final: 0.7949 (OUTLIER) REVERT: I 78 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7826 (tm) REVERT: J 77 SER cc_start: 0.8061 (t) cc_final: 0.7498 (p) REVERT: J 95 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7648 (pp) outliers start: 57 outliers final: 25 residues processed: 529 average time/residue: 0.4570 time to fit residues: 277.0699 Evaluate side-chains 468 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 437 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 392 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain M residue 7 SER 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 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 307 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 12 SER 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 155 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 121 optimal weight: 0.3980 chunk 179 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 136 GLN A 147 ASN A 199 ASN A 226 GLN A 441 ASN N 55 GLN B 93 ASN B 136 GLN B 199 ASN B 441 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN E 93 ASN E 226 GLN E 441 ASN H 86 ASN H 441 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.095341 restraints weight = 27816.541| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.90 r_work: 0.2985 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20032 Z= 0.136 Angle : 0.603 6.406 27248 Z= 0.316 Chirality : 0.045 0.139 2952 Planarity : 0.005 0.049 3476 Dihedral : 5.645 43.858 3060 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.30 % Favored : 93.54 % Rotamer: Outliers : 3.68 % Allowed : 13.68 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.15), residues: 2460 helix: -1.63 (0.78), residues: 24 sheet: -0.20 (0.18), residues: 884 loop : -2.65 (0.12), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.015 0.001 TYR E 121 PHE 0.017 0.002 PHE E 410 TRP 0.016 0.001 TRP E 178 HIS 0.003 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00316 (19972) covalent geometry : angle 0.59228 (27112) SS BOND : bond 0.00473 ( 44) SS BOND : angle 1.16303 ( 88) hydrogen bonds : bond 0.04147 ( 552) hydrogen bonds : angle 5.82940 ( 1620) link_NAG-ASN : bond 0.00196 ( 16) link_NAG-ASN : angle 2.35139 ( 48) *********************** 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 528 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 450 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 239 VAL cc_start: 0.8182 (p) cc_final: 0.7981 (t) REVERT: A 247 SER cc_start: 0.8331 (m) cc_final: 0.8103 (p) REVERT: A 356 ASP cc_start: 0.8145 (t0) cc_final: 0.7914 (t0) REVERT: A 457 SER cc_start: 0.8500 (t) cc_final: 0.8289 (m) REVERT: A 464 ILE cc_start: 0.8131 (pt) cc_final: 0.7871 (mm) REVERT: M 56 ILE cc_start: 0.8630 (mt) cc_final: 0.8336 (mt) REVERT: M 100 THR cc_start: 0.9102 (t) cc_final: 0.8876 (t) REVERT: N 46 LEU cc_start: 0.8774 (tp) cc_final: 0.8459 (tp) REVERT: N 92 ASP cc_start: 0.8353 (t0) cc_final: 0.7919 (t0) REVERT: N 95 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7634 (pp) REVERT: B 213 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: B 247 SER cc_start: 0.8353 (m) cc_final: 0.8122 (p) REVERT: B 249 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7866 (mtpp) REVERT: B 362 MET cc_start: 0.8554 (ptm) cc_final: 0.8087 (ptp) REVERT: B 389 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8660 (mttt) REVERT: B 391 GLN cc_start: 0.8356 (pt0) cc_final: 0.8070 (pt0) REVERT: B 393 ASN cc_start: 0.8553 (m110) cc_final: 0.8174 (m-40) REVERT: B 457 SER cc_start: 0.8526 (t) cc_final: 0.8319 (m) REVERT: C 100 THR cc_start: 0.8948 (t) cc_final: 0.8734 (t) REVERT: D 46 LEU cc_start: 0.8692 (tp) cc_final: 0.8416 (tp) REVERT: D 92 ASP cc_start: 0.8291 (t0) cc_final: 0.7786 (t0) REVERT: D 93 SER cc_start: 0.8085 (p) cc_final: 0.7746 (p) REVERT: D 95 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7402 (pp) REVERT: E 102 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8523 (tttp) REVERT: E 147 ASN cc_start: 0.8057 (m-40) cc_final: 0.7698 (m110) REVERT: E 210 ARG cc_start: 0.8397 (ptp90) cc_final: 0.8151 (ptp-110) REVERT: E 213 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: E 393 ASN cc_start: 0.8468 (m110) cc_final: 0.8133 (m-40) REVERT: E 443 ILE cc_start: 0.8045 (pt) cc_final: 0.7842 (tt) REVERT: E 457 SER cc_start: 0.8491 (t) cc_final: 0.8283 (m) REVERT: F 56 ILE cc_start: 0.8687 (mt) cc_final: 0.8441 (mt) REVERT: F 100 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7771 (ttp-170) REVERT: H 113 ASP cc_start: 0.7444 (m-30) cc_final: 0.7207 (m-30) REVERT: H 147 ASN cc_start: 0.8179 (m-40) cc_final: 0.7845 (m110) REVERT: H 210 ARG cc_start: 0.8467 (ptp90) cc_final: 0.8210 (ptp-110) REVERT: H 239 VAL cc_start: 0.8296 (p) cc_final: 0.8046 (t) REVERT: H 247 SER cc_start: 0.8314 (m) cc_final: 0.8051 (p) REVERT: H 389 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8588 (mttt) REVERT: J 45 ASN cc_start: 0.8357 (m-40) cc_final: 0.8142 (t0) REVERT: J 77 SER cc_start: 0.8133 (t) cc_final: 0.7894 (t) outliers start: 78 outliers final: 37 residues processed: 498 average time/residue: 0.4727 time to fit residues: 268.8849 Evaluate side-chains 479 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 433 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain A residue 329 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 95 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 95 LEU 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 389 LYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 7 SER 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 213 ASP Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 265 ILE 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 100 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 48 ILE 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 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 184 HIS A 199 ASN A 226 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 184 HIS B 199 ASN E 93 ASN E 136 GLN E 184 HIS E 226 GLN H 136 GLN H 184 HIS H 226 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.090213 restraints weight = 28065.874| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.92 r_work: 0.2945 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20032 Z= 0.184 Angle : 0.634 6.501 27248 Z= 0.334 Chirality : 0.046 0.161 2952 Planarity : 0.005 0.050 3476 Dihedral : 5.363 21.563 3048 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.38 % Favored : 93.46 % Rotamer: Outliers : 3.96 % Allowed : 14.81 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.15), residues: 2460 helix: -0.88 (0.89), residues: 24 sheet: -0.05 (0.18), residues: 868 loop : -2.61 (0.12), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 283 TYR 0.018 0.002 TYR A 121 PHE 0.019 0.002 PHE E 410 TRP 0.024 0.002 TRP H 178 HIS 0.004 0.001 HIS H 144 Details of bonding type rmsd covalent geometry : bond 0.00441 (19972) covalent geometry : angle 0.62188 (27112) SS BOND : bond 0.00529 ( 44) SS BOND : angle 1.42064 ( 88) hydrogen bonds : bond 0.04358 ( 552) hydrogen bonds : angle 5.77736 ( 1620) link_NAG-ASN : bond 0.00190 ( 16) link_NAG-ASN : angle 2.41879 ( 48) *********************** 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 524 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 440 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8028 (m-40) cc_final: 0.7709 (m110) REVERT: A 239 VAL cc_start: 0.8255 (p) cc_final: 0.8041 (t) REVERT: A 247 SER cc_start: 0.8430 (m) cc_final: 0.8189 (p) REVERT: A 356 ASP cc_start: 0.8163 (t0) cc_final: 0.7944 (t0) REVERT: A 369 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8393 (m) REVERT: A 457 SER cc_start: 0.8549 (t) cc_final: 0.8334 (m) REVERT: N 45 ASN cc_start: 0.8439 (m-40) cc_final: 0.8210 (t0) REVERT: N 46 LEU cc_start: 0.8789 (tp) cc_final: 0.8511 (tp) REVERT: N 61 ARG cc_start: 0.8198 (ptt180) cc_final: 0.7876 (ptt90) REVERT: N 92 ASP cc_start: 0.8417 (t0) cc_final: 0.7951 (t0) REVERT: N 95 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7660 (pp) REVERT: B 119 GLU cc_start: 0.7947 (mp0) cc_final: 0.7514 (mp0) REVERT: B 147 ASN cc_start: 0.7948 (m110) cc_final: 0.7652 (m110) REVERT: B 213 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: B 247 SER cc_start: 0.8376 (m) cc_final: 0.8140 (p) REVERT: B 249 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7870 (mtpp) REVERT: B 362 MET cc_start: 0.8554 (ptm) cc_final: 0.8138 (ptp) REVERT: B 389 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8673 (mttt) REVERT: B 391 GLN cc_start: 0.8411 (pt0) cc_final: 0.8098 (pt0) REVERT: B 393 ASN cc_start: 0.8520 (m110) cc_final: 0.8229 (m-40) REVERT: B 463 ASP cc_start: 0.7998 (t0) cc_final: 0.7766 (t0) REVERT: D 46 LEU cc_start: 0.8707 (tp) cc_final: 0.8387 (tp) REVERT: D 92 ASP cc_start: 0.8382 (t0) cc_final: 0.7872 (t0) REVERT: D 93 SER cc_start: 0.8104 (p) cc_final: 0.7773 (p) REVERT: D 95 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7454 (pp) REVERT: E 147 ASN cc_start: 0.8099 (m-40) cc_final: 0.7764 (m110) REVERT: E 210 ARG cc_start: 0.8360 (ptp90) cc_final: 0.8083 (ptp-110) REVERT: E 213 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: E 255 LEU cc_start: 0.8655 (mp) cc_final: 0.8441 (mt) REVERT: E 356 ASP cc_start: 0.8109 (t0) cc_final: 0.7903 (t0) REVERT: E 393 ASN cc_start: 0.8487 (m110) cc_final: 0.8162 (m-40) REVERT: F 100 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7740 (ttp-170) REVERT: H 113 ASP cc_start: 0.7518 (m-30) cc_final: 0.7250 (m-30) REVERT: H 147 ASN cc_start: 0.8164 (m-40) cc_final: 0.7806 (m110) REVERT: H 210 ARG cc_start: 0.8428 (ptp90) cc_final: 0.8141 (ptp-110) REVERT: H 239 VAL cc_start: 0.8237 (p) cc_final: 0.8023 (t) REVERT: H 247 SER cc_start: 0.8306 (m) cc_final: 0.8071 (p) REVERT: H 389 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8605 (mttt) REVERT: J 45 ASN cc_start: 0.8385 (m-40) cc_final: 0.8122 (t0) REVERT: J 77 SER cc_start: 0.8422 (t) cc_final: 0.7898 (p) outliers start: 84 outliers final: 46 residues processed: 481 average time/residue: 0.4831 time to fit residues: 264.8546 Evaluate side-chains 473 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 271 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 369 THR 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 51 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 95 LEU 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 389 LYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 199 ASN 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 312 ILE 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 51 LEU 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 95 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 249 LYS Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 389 LYS 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 49 SER Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 54 LEU 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 205 optimal weight: 3.9990 chunk 219 optimal weight: 0.0070 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.0060 overall best weight: 0.5014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 199 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 199 ASN E 86 ASN E 93 ASN E 136 GLN E 226 GLN H 226 GLN ** H 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094353 restraints weight = 27946.207| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.92 r_work: 0.2975 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20032 Z= 0.108 Angle : 0.554 6.391 27248 Z= 0.291 Chirality : 0.044 0.143 2952 Planarity : 0.004 0.048 3476 Dihedral : 4.880 20.737 3048 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.11 % Rotamer: Outliers : 3.63 % Allowed : 15.66 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.15), residues: 2460 helix: -0.10 (1.03), residues: 24 sheet: 0.19 (0.18), residues: 880 loop : -2.41 (0.13), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 283 TYR 0.019 0.001 TYR N 94 PHE 0.015 0.001 PHE E 410 TRP 0.018 0.001 TRP E 178 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00248 (19972) covalent geometry : angle 0.54520 (27112) SS BOND : bond 0.00378 ( 44) SS BOND : angle 1.11772 ( 88) hydrogen bonds : bond 0.03480 ( 552) hydrogen bonds : angle 5.43533 ( 1620) link_NAG-ASN : bond 0.00187 ( 16) link_NAG-ASN : angle 2.08276 ( 48) *********************** 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 519 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 442 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8020 (m-40) cc_final: 0.7713 (m110) REVERT: A 239 VAL cc_start: 0.8253 (p) cc_final: 0.8038 (t) REVERT: A 247 SER cc_start: 0.8400 (m) cc_final: 0.8150 (p) REVERT: M 87 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7506 (p) REVERT: N 45 ASN cc_start: 0.8441 (m-40) cc_final: 0.8221 (t0) REVERT: N 46 LEU cc_start: 0.8752 (tp) cc_final: 0.8370 (tp) REVERT: N 61 ARG cc_start: 0.8205 (ptt180) cc_final: 0.7928 (ptt90) REVERT: N 77 SER cc_start: 0.8027 (t) cc_final: 0.7801 (t) REVERT: N 92 ASP cc_start: 0.8368 (t0) cc_final: 0.7931 (t0) REVERT: N 95 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7630 (pp) REVERT: B 119 GLU cc_start: 0.7975 (mp0) cc_final: 0.7580 (mp0) REVERT: B 147 ASN cc_start: 0.7879 (m110) cc_final: 0.7606 (m110) REVERT: B 232 CYS cc_start: 0.7568 (m) cc_final: 0.7347 (m) REVERT: B 247 SER cc_start: 0.8343 (m) cc_final: 0.8078 (p) REVERT: B 329 SER cc_start: 0.8328 (t) cc_final: 0.8017 (m) REVERT: B 389 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8656 (mttt) REVERT: B 391 GLN cc_start: 0.8368 (pt0) cc_final: 0.8077 (pt0) REVERT: B 393 ASN cc_start: 0.8522 (m110) cc_final: 0.8242 (m-40) REVERT: B 463 ASP cc_start: 0.7990 (t0) cc_final: 0.7714 (t0) REVERT: C 102 LEU cc_start: 0.8247 (pp) cc_final: 0.8029 (pt) REVERT: D 46 LEU cc_start: 0.8689 (tp) cc_final: 0.8395 (tp) REVERT: D 92 ASP cc_start: 0.8349 (t0) cc_final: 0.7869 (t0) REVERT: D 93 SER cc_start: 0.8089 (p) cc_final: 0.7758 (p) REVERT: D 95 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7391 (pp) REVERT: E 147 ASN cc_start: 0.8106 (m-40) cc_final: 0.7784 (m110) REVERT: E 210 ARG cc_start: 0.8339 (ptp90) cc_final: 0.8078 (ptp-110) REVERT: E 255 LEU cc_start: 0.8677 (mp) cc_final: 0.8477 (mt) REVERT: E 356 ASP cc_start: 0.8047 (t0) cc_final: 0.7838 (t0) REVERT: E 392 THR cc_start: 0.8272 (t) cc_final: 0.7795 (m) REVERT: E 393 ASN cc_start: 0.8478 (m110) cc_final: 0.8184 (m-40) REVERT: E 431 LYS cc_start: 0.7799 (tppt) cc_final: 0.7468 (tppt) REVERT: F 96 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8456 (t) REVERT: G 77 SER cc_start: 0.8524 (t) cc_final: 0.8054 (p) REVERT: H 113 ASP cc_start: 0.7531 (m-30) cc_final: 0.7275 (m-30) REVERT: H 147 ASN cc_start: 0.8155 (m-40) cc_final: 0.7795 (m110) REVERT: H 210 ARG cc_start: 0.8403 (ptp90) cc_final: 0.8132 (ptp-110) REVERT: H 247 SER cc_start: 0.8334 (m) cc_final: 0.8081 (p) REVERT: J 45 ASN cc_start: 0.8329 (m-40) cc_final: 0.8120 (t0) REVERT: J 77 SER cc_start: 0.8407 (t) cc_final: 0.7862 (p) REVERT: J 92 ASP cc_start: 0.8414 (t0) cc_final: 0.7953 (t0) outliers start: 77 outliers final: 43 residues processed: 485 average time/residue: 0.5193 time to fit residues: 286.8878 Evaluate side-chains 477 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 429 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 329 SER Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 467 MET 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 48 ILE Chi-restraints excluded: chain N residue 95 LEU 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 389 LYS 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 199 ASN 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 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 45 ASN 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 249 LYS Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain H residue 329 SER 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 54 LEU 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 107 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 202 optimal weight: 0.4980 chunk 185 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 294 ASN E 93 ASN E 136 GLN E 226 GLN H 226 GLN ** H 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093507 restraints weight = 27833.079| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.90 r_work: 0.2969 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20032 Z= 0.146 Angle : 0.585 6.393 27248 Z= 0.308 Chirality : 0.045 0.149 2952 Planarity : 0.004 0.048 3476 Dihedral : 4.956 20.398 3048 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.14 % Favored : 93.70 % Rotamer: Outliers : 4.15 % Allowed : 15.80 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.16), residues: 2460 helix: -0.09 (1.03), residues: 24 sheet: 0.26 (0.18), residues: 864 loop : -2.40 (0.13), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.023 0.002 TYR N 94 PHE 0.017 0.002 PHE E 410 TRP 0.021 0.001 TRP E 178 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00346 (19972) covalent geometry : angle 0.57503 (27112) SS BOND : bond 0.00468 ( 44) SS BOND : angle 1.26272 ( 88) hydrogen bonds : bond 0.03850 ( 552) hydrogen bonds : angle 5.49302 ( 1620) link_NAG-ASN : bond 0.00187 ( 16) link_NAG-ASN : angle 2.20425 ( 48) *********************** 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 535 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 447 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8056 (m-40) cc_final: 0.7739 (m110) REVERT: A 239 VAL cc_start: 0.8267 (p) cc_final: 0.8054 (t) REVERT: A 247 SER cc_start: 0.8400 (m) cc_final: 0.8174 (p) REVERT: A 356 ASP cc_start: 0.7932 (t0) cc_final: 0.7707 (t0) REVERT: A 369 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8403 (m) REVERT: A 431 LYS cc_start: 0.7863 (tppt) cc_final: 0.7526 (tppt) REVERT: A 443 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (tt) REVERT: M 100 THR cc_start: 0.9048 (t) cc_final: 0.8836 (t) REVERT: N 45 ASN cc_start: 0.8440 (m-40) cc_final: 0.8215 (t0) REVERT: N 46 LEU cc_start: 0.8789 (tp) cc_final: 0.8524 (tp) REVERT: N 77 SER cc_start: 0.8043 (t) cc_final: 0.7775 (t) REVERT: N 92 ASP cc_start: 0.8388 (t0) cc_final: 0.7950 (t0) REVERT: N 95 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7686 (pp) REVERT: B 119 GLU cc_start: 0.7982 (mp0) cc_final: 0.7602 (mp0) REVERT: B 147 ASN cc_start: 0.7917 (m110) cc_final: 0.7608 (m110) REVERT: B 213 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: B 232 CYS cc_start: 0.7590 (m) cc_final: 0.7355 (m) REVERT: B 247 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 389 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8692 (mttt) REVERT: B 391 GLN cc_start: 0.8412 (pt0) cc_final: 0.8126 (pt0) REVERT: B 393 ASN cc_start: 0.8514 (m110) cc_final: 0.8186 (m-40) REVERT: B 463 ASP cc_start: 0.7989 (t0) cc_final: 0.7728 (t0) REVERT: C 87 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7485 (p) REVERT: C 102 LEU cc_start: 0.8299 (pp) cc_final: 0.8069 (pt) REVERT: D 46 LEU cc_start: 0.8708 (tp) cc_final: 0.8394 (tp) REVERT: D 92 ASP cc_start: 0.8383 (t0) cc_final: 0.7914 (t0) REVERT: D 93 SER cc_start: 0.8122 (p) cc_final: 0.7867 (p) REVERT: D 95 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7486 (pp) REVERT: E 147 ASN cc_start: 0.8125 (m-40) cc_final: 0.7787 (m110) REVERT: E 210 ARG cc_start: 0.8338 (ptp90) cc_final: 0.8073 (ptp-110) REVERT: E 213 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: E 392 THR cc_start: 0.8258 (t) cc_final: 0.7967 (m) REVERT: E 415 LYS cc_start: 0.8500 (tttt) cc_final: 0.8290 (tttt) REVERT: E 431 LYS cc_start: 0.7830 (tppt) cc_final: 0.7507 (tppt) REVERT: F 87 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7532 (p) REVERT: G 61 ARG cc_start: 0.8268 (ptp90) cc_final: 0.7849 (ptp90) REVERT: G 77 SER cc_start: 0.8562 (t) cc_final: 0.8051 (p) REVERT: G 92 ASP cc_start: 0.8364 (t0) cc_final: 0.7930 (t0) REVERT: H 113 ASP cc_start: 0.7542 (m-30) cc_final: 0.7255 (m-30) REVERT: H 147 ASN cc_start: 0.8138 (m-40) cc_final: 0.7767 (m110) REVERT: H 210 ARG cc_start: 0.8433 (ptp90) cc_final: 0.8153 (ptp-110) REVERT: H 247 SER cc_start: 0.8311 (m) cc_final: 0.8077 (p) REVERT: H 389 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8634 (mttt) REVERT: H 392 THR cc_start: 0.8487 (m) cc_final: 0.8150 (t) REVERT: J 61 ARG cc_start: 0.8388 (ptp90) cc_final: 0.8008 (ptp90) REVERT: J 77 SER cc_start: 0.8487 (t) cc_final: 0.7906 (p) REVERT: J 92 ASP cc_start: 0.8455 (t0) cc_final: 0.8044 (t0) outliers start: 88 outliers final: 50 residues processed: 491 average time/residue: 0.5222 time to fit residues: 292.2290 Evaluate side-chains 493 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 432 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE 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 108 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 95 LEU 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 329 SER Chi-restraints excluded: chain B residue 389 LYS 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 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 199 ASN 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 356 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 45 ASN Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 249 LYS Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain H residue 311 SER Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 389 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 54 LEU 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 163 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN E 93 ASN E 136 GLN E 226 GLN E 393 ASN H 226 GLN J 45 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091977 restraints weight = 28094.173| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.93 r_work: 0.2945 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20032 Z= 0.194 Angle : 0.624 6.424 27248 Z= 0.330 Chirality : 0.047 0.203 2952 Planarity : 0.005 0.049 3476 Dihedral : 5.168 20.757 3048 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.26 % Favored : 93.58 % Rotamer: Outliers : 4.20 % Allowed : 16.04 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.16), residues: 2460 helix: -0.25 (1.02), residues: 24 sheet: 0.28 (0.18), residues: 860 loop : -2.36 (0.13), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 61 TYR 0.027 0.002 TYR N 94 PHE 0.019 0.002 PHE B 410 TRP 0.023 0.002 TRP H 178 HIS 0.003 0.001 HIS H 144 Details of bonding type rmsd covalent geometry : bond 0.00467 (19972) covalent geometry : angle 0.61232 (27112) SS BOND : bond 0.00540 ( 44) SS BOND : angle 1.47324 ( 88) hydrogen bonds : bond 0.04256 ( 552) hydrogen bonds : angle 5.61973 ( 1620) link_NAG-ASN : bond 0.00222 ( 16) link_NAG-ASN : angle 2.32426 ( 48) *********************** 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 523 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 434 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8060 (m-40) cc_final: 0.7758 (m110) REVERT: A 239 VAL cc_start: 0.8284 (p) cc_final: 0.8077 (t) REVERT: A 247 SER cc_start: 0.8443 (m) cc_final: 0.8202 (p) REVERT: A 294 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8462 (t0) REVERT: A 356 ASP cc_start: 0.8019 (t0) cc_final: 0.7795 (t0) REVERT: A 431 LYS cc_start: 0.7862 (tppt) cc_final: 0.7516 (tppt) REVERT: N 45 ASN cc_start: 0.8438 (m-40) cc_final: 0.8203 (t0) REVERT: N 46 LEU cc_start: 0.8793 (tp) cc_final: 0.8511 (tp) REVERT: N 77 SER cc_start: 0.8332 (t) cc_final: 0.7823 (p) REVERT: N 92 ASP cc_start: 0.8403 (t0) cc_final: 0.7976 (t0) REVERT: N 95 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7730 (pp) REVERT: B 119 GLU cc_start: 0.8003 (mp0) cc_final: 0.7566 (mp0) REVERT: B 147 ASN cc_start: 0.7911 (m110) cc_final: 0.7610 (m110) REVERT: B 213 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: B 232 CYS cc_start: 0.7616 (m) cc_final: 0.7357 (m) REVERT: B 247 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8120 (p) REVERT: B 389 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8706 (mttt) REVERT: B 391 GLN cc_start: 0.8444 (pt0) cc_final: 0.8141 (pt0) REVERT: B 393 ASN cc_start: 0.8495 (m110) cc_final: 0.8170 (m-40) REVERT: B 463 ASP cc_start: 0.8031 (t0) cc_final: 0.7711 (t0) REVERT: C 28 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7692 (ttmm) REVERT: C 87 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7537 (p) REVERT: C 100 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7939 (ttp-170) REVERT: D 92 ASP cc_start: 0.8399 (t0) cc_final: 0.7930 (t0) REVERT: D 93 SER cc_start: 0.8121 (p) cc_final: 0.7804 (p) REVERT: D 95 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7463 (pp) REVERT: E 147 ASN cc_start: 0.8149 (m-40) cc_final: 0.7819 (m110) REVERT: E 210 ARG cc_start: 0.8336 (ptp90) cc_final: 0.8062 (ptp-110) REVERT: E 415 LYS cc_start: 0.8509 (tttt) cc_final: 0.8296 (tttt) REVERT: F 87 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7580 (p) REVERT: G 77 SER cc_start: 0.8565 (t) cc_final: 0.8070 (p) REVERT: G 92 ASP cc_start: 0.8380 (t0) cc_final: 0.7961 (t0) REVERT: H 113 ASP cc_start: 0.7577 (m-30) cc_final: 0.7268 (m-30) REVERT: H 147 ASN cc_start: 0.8158 (m-40) cc_final: 0.7795 (m110) REVERT: H 210 ARG cc_start: 0.8431 (ptp90) cc_final: 0.8146 (ptp-110) REVERT: H 247 SER cc_start: 0.8338 (m) cc_final: 0.8095 (p) REVERT: H 389 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8637 (mttt) REVERT: H 392 THR cc_start: 0.8524 (m) cc_final: 0.8170 (t) REVERT: J 45 ASN cc_start: 0.8366 (m-40) cc_final: 0.8026 (t0) REVERT: J 77 SER cc_start: 0.8391 (t) cc_final: 0.7821 (p) REVERT: J 92 ASP cc_start: 0.8485 (t0) cc_final: 0.8089 (t0) outliers start: 89 outliers final: 55 residues processed: 475 average time/residue: 0.4812 time to fit residues: 262.1519 Evaluate side-chains 495 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 429 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 294 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE 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 48 ILE 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 261 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 389 LYS 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 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 199 ASN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 307 VAL 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 46 GLU 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 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 249 LYS Chi-restraints excluded: chain H residue 311 SER Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 389 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 54 LEU 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 152 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 228 optimal weight: 0.4980 chunk 160 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN E 93 ASN 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 = 0.3349 r_free = 0.3349 target = 0.111127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092877 restraints weight = 27974.781| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.93 r_work: 0.2958 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20032 Z= 0.146 Angle : 0.593 7.218 27248 Z= 0.311 Chirality : 0.046 0.306 2952 Planarity : 0.004 0.048 3476 Dihedral : 4.988 20.261 3048 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 3.73 % Allowed : 16.79 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.16), residues: 2460 helix: -0.02 (1.06), residues: 24 sheet: 0.40 (0.18), residues: 908 loop : -2.34 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.025 0.001 TYR N 94 PHE 0.017 0.002 PHE A 410 TRP 0.021 0.002 TRP E 178 HIS 0.003 0.001 HIS H 144 Details of bonding type rmsd covalent geometry : bond 0.00346 (19972) covalent geometry : angle 0.58131 (27112) SS BOND : bond 0.00460 ( 44) SS BOND : angle 1.47283 ( 88) hydrogen bonds : bond 0.03786 ( 552) hydrogen bonds : angle 5.49921 ( 1620) link_NAG-ASN : bond 0.00178 ( 16) link_NAG-ASN : angle 2.14010 ( 48) *********************** 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 519 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 440 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8047 (m-40) cc_final: 0.7735 (m110) REVERT: A 239 VAL cc_start: 0.8276 (p) cc_final: 0.8066 (t) REVERT: A 247 SER cc_start: 0.8431 (m) cc_final: 0.8196 (p) REVERT: A 431 LYS cc_start: 0.7840 (tppt) cc_final: 0.7496 (tppt) REVERT: M 87 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7571 (p) REVERT: N 45 ASN cc_start: 0.8426 (m-40) cc_final: 0.8223 (t0) REVERT: N 46 LEU cc_start: 0.8789 (tp) cc_final: 0.8557 (tp) REVERT: N 77 SER cc_start: 0.8281 (t) cc_final: 0.7821 (p) REVERT: N 92 ASP cc_start: 0.8369 (t0) cc_final: 0.7934 (t0) REVERT: N 95 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7688 (pp) REVERT: B 119 GLU cc_start: 0.8002 (mp0) cc_final: 0.7572 (mp0) REVERT: B 147 ASN cc_start: 0.7897 (m110) cc_final: 0.7585 (m110) REVERT: B 232 CYS cc_start: 0.7523 (m) cc_final: 0.7273 (m) REVERT: B 247 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8089 (p) REVERT: B 389 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8695 (mttt) REVERT: B 391 GLN cc_start: 0.8426 (pt0) cc_final: 0.8117 (pt0) REVERT: B 393 ASN cc_start: 0.8502 (m110) cc_final: 0.8214 (m-40) REVERT: B 463 ASP cc_start: 0.8010 (t0) cc_final: 0.7729 (t0) REVERT: C 87 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7509 (p) REVERT: C 100 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7882 (ttp-170) REVERT: D 92 ASP cc_start: 0.8380 (t0) cc_final: 0.7961 (t0) REVERT: D 93 SER cc_start: 0.8133 (p) cc_final: 0.7883 (p) REVERT: D 95 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7436 (pp) REVERT: E 147 ASN cc_start: 0.8135 (m-40) cc_final: 0.7819 (m110) REVERT: E 210 ARG cc_start: 0.8346 (ptp90) cc_final: 0.8080 (ptp-110) REVERT: E 415 LYS cc_start: 0.8482 (tttt) cc_final: 0.8276 (tttt) REVERT: E 431 LYS cc_start: 0.7811 (tppt) cc_final: 0.7458 (tppt) REVERT: F 87 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7560 (p) REVERT: G 61 ARG cc_start: 0.8227 (ptp90) cc_final: 0.7816 (ptp90) REVERT: G 77 SER cc_start: 0.8528 (t) cc_final: 0.8015 (p) REVERT: G 92 ASP cc_start: 0.8380 (t0) cc_final: 0.7961 (t0) REVERT: H 113 ASP cc_start: 0.7580 (m-30) cc_final: 0.7266 (m-30) REVERT: H 147 ASN cc_start: 0.8148 (m-40) cc_final: 0.7777 (m110) REVERT: H 210 ARG cc_start: 0.8427 (ptp90) cc_final: 0.8143 (ptp-110) REVERT: H 222 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7187 (mm) REVERT: H 247 SER cc_start: 0.8325 (m) cc_final: 0.8099 (p) REVERT: H 389 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8625 (mttt) REVERT: H 392 THR cc_start: 0.8509 (m) cc_final: 0.8143 (t) REVERT: I 87 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7451 (p) REVERT: J 61 ARG cc_start: 0.8319 (ptp90) cc_final: 0.7926 (ptp90) REVERT: J 77 SER cc_start: 0.8396 (t) cc_final: 0.7859 (p) REVERT: J 92 ASP cc_start: 0.8465 (t0) cc_final: 0.8051 (t0) outliers start: 79 outliers final: 51 residues processed: 479 average time/residue: 0.4988 time to fit residues: 273.3092 Evaluate side-chains 492 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 430 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE 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 48 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 202 THR 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 389 LYS 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 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 199 ASN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 385 LYS 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 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 249 LYS Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 389 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 87 THR 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 95 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 5.9990 chunk 205 optimal weight: 0.0670 chunk 51 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 124 optimal weight: 0.4980 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 136 GLN E 226 GLN H 226 GLN J 45 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093361 restraints weight = 27944.408| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.93 r_work: 0.2967 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20032 Z= 0.131 Angle : 0.580 7.089 27248 Z= 0.303 Chirality : 0.045 0.154 2952 Planarity : 0.004 0.047 3476 Dihedral : 4.884 20.130 3048 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 3.77 % Allowed : 17.08 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.16), residues: 2460 helix: 0.12 (1.08), residues: 24 sheet: 0.40 (0.18), residues: 932 loop : -2.29 (0.13), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.027 0.001 TYR N 94 PHE 0.016 0.002 PHE A 410 TRP 0.020 0.001 TRP E 178 HIS 0.003 0.001 HIS H 144 Details of bonding type rmsd covalent geometry : bond 0.00309 (19972) covalent geometry : angle 0.56998 (27112) SS BOND : bond 0.00438 ( 44) SS BOND : angle 1.25923 ( 88) hydrogen bonds : bond 0.03625 ( 552) hydrogen bonds : angle 5.41707 ( 1620) link_NAG-ASN : bond 0.00196 ( 16) link_NAG-ASN : angle 2.06451 ( 48) *********************** 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 505 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 425 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8074 (m-40) cc_final: 0.7766 (m110) REVERT: A 247 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 416 SER cc_start: 0.8519 (m) cc_final: 0.8310 (t) REVERT: A 431 LYS cc_start: 0.7836 (tppt) cc_final: 0.7476 (tppt) REVERT: M 78 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8210 (tt) REVERT: M 87 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7560 (p) REVERT: N 46 LEU cc_start: 0.8767 (tp) cc_final: 0.8542 (tp) REVERT: N 92 ASP cc_start: 0.8366 (t0) cc_final: 0.7956 (t0) REVERT: N 95 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7673 (pp) REVERT: B 119 GLU cc_start: 0.8002 (mp0) cc_final: 0.7571 (mp0) REVERT: B 147 ASN cc_start: 0.7906 (m110) cc_final: 0.7630 (m110) REVERT: B 213 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: B 232 CYS cc_start: 0.7541 (m) cc_final: 0.7285 (m) REVERT: B 247 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8105 (p) REVERT: B 389 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8652 (mttt) REVERT: B 391 GLN cc_start: 0.8385 (pt0) cc_final: 0.8081 (pt0) REVERT: B 393 ASN cc_start: 0.8506 (m110) cc_final: 0.8229 (m-40) REVERT: B 416 SER cc_start: 0.8443 (m) cc_final: 0.8211 (t) REVERT: B 463 ASP cc_start: 0.8021 (t0) cc_final: 0.7711 (t0) REVERT: C 28 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7647 (ttmm) REVERT: C 87 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7491 (p) REVERT: C 100 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7834 (ttp-170) REVERT: C 102 LEU cc_start: 0.8345 (pp) cc_final: 0.8072 (pt) REVERT: D 92 ASP cc_start: 0.8390 (t0) cc_final: 0.7925 (t0) REVERT: D 93 SER cc_start: 0.8144 (p) cc_final: 0.7899 (p) REVERT: D 95 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7452 (pp) REVERT: E 147 ASN cc_start: 0.8125 (m-40) cc_final: 0.7812 (m110) REVERT: E 210 ARG cc_start: 0.8345 (ptp90) cc_final: 0.8082 (ptp-110) REVERT: E 213 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: E 415 LYS cc_start: 0.8472 (tttt) cc_final: 0.8217 (tttt) REVERT: E 416 SER cc_start: 0.8590 (m) cc_final: 0.8339 (t) REVERT: E 431 LYS cc_start: 0.7804 (tppt) cc_final: 0.7450 (tppt) REVERT: F 87 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7547 (p) REVERT: G 61 ARG cc_start: 0.8223 (ptp90) cc_final: 0.7771 (ptp90) REVERT: G 77 SER cc_start: 0.8472 (t) cc_final: 0.7958 (p) REVERT: G 92 ASP cc_start: 0.8364 (t0) cc_final: 0.7944 (t0) REVERT: H 113 ASP cc_start: 0.7582 (m-30) cc_final: 0.7271 (m-30) REVERT: H 147 ASN cc_start: 0.8152 (m-40) cc_final: 0.7796 (m110) REVERT: H 210 ARG cc_start: 0.8424 (ptp90) cc_final: 0.8138 (ptp-110) REVERT: H 222 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7181 (mm) REVERT: H 247 SER cc_start: 0.8319 (m) cc_final: 0.8069 (p) REVERT: H 389 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8585 (mttt) REVERT: H 392 THR cc_start: 0.8505 (m) cc_final: 0.8142 (t) REVERT: I 63 VAL cc_start: 0.8392 (m) cc_final: 0.8013 (t) REVERT: I 87 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7401 (p) REVERT: J 61 ARG cc_start: 0.8333 (ptp90) cc_final: 0.7930 (ptp90) REVERT: J 77 SER cc_start: 0.8398 (t) cc_final: 0.7806 (p) REVERT: J 92 ASP cc_start: 0.8439 (t0) cc_final: 0.8016 (t0) outliers start: 80 outliers final: 56 residues processed: 465 average time/residue: 0.5081 time to fit residues: 269.3564 Evaluate side-chains 495 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 423 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 SER 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 442 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE 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 78 LEU 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 48 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 106 ILE 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 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 389 LYS 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 199 ASN 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 385 LYS 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 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 199 ASN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 249 LYS Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 389 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 87 THR 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 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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 6 GLN B 93 ASN D 6 GLN E 136 GLN E 226 GLN G 6 GLN H 226 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.092141 restraints weight = 28086.601| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.93 r_work: 0.2949 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20032 Z= 0.198 Angle : 0.642 7.089 27248 Z= 0.338 Chirality : 0.047 0.164 2952 Planarity : 0.005 0.049 3476 Dihedral : 5.168 21.439 3048 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 3.87 % Allowed : 17.31 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.16), residues: 2460 helix: -0.12 (1.06), residues: 24 sheet: 0.39 (0.18), residues: 884 loop : -2.37 (0.13), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 61 TYR 0.030 0.002 TYR N 94 PHE 0.020 0.002 PHE A 410 TRP 0.022 0.002 TRP H 178 HIS 0.003 0.001 HIS J 90 Details of bonding type rmsd covalent geometry : bond 0.00477 (19972) covalent geometry : angle 0.62949 (27112) SS BOND : bond 0.00561 ( 44) SS BOND : angle 1.60273 ( 88) hydrogen bonds : bond 0.04238 ( 552) hydrogen bonds : angle 5.57754 ( 1620) link_NAG-ASN : bond 0.00240 ( 16) link_NAG-ASN : angle 2.32703 ( 48) ********************** 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: 82 poor density : 434 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8056 (m-40) cc_final: 0.7749 (m110) REVERT: A 247 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 431 LYS cc_start: 0.7863 (tppt) cc_final: 0.7512 (tppt) REVERT: N 46 LEU cc_start: 0.8794 (tp) cc_final: 0.8552 (tp) REVERT: N 92 ASP cc_start: 0.8416 (t0) cc_final: 0.7992 (t0) REVERT: N 95 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7706 (pp) REVERT: B 119 GLU cc_start: 0.8010 (mp0) cc_final: 0.7602 (mp0) REVERT: B 147 ASN cc_start: 0.7918 (m110) cc_final: 0.7630 (m110) REVERT: B 213 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: B 232 CYS cc_start: 0.7560 (m) cc_final: 0.7299 (m) REVERT: B 389 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8678 (mttt) REVERT: B 391 GLN cc_start: 0.8373 (pt0) cc_final: 0.8057 (pt0) REVERT: B 393 ASN cc_start: 0.8512 (m110) cc_final: 0.8230 (m-40) REVERT: B 416 SER cc_start: 0.8617 (m) cc_final: 0.8370 (t) REVERT: B 463 ASP cc_start: 0.8032 (t0) cc_final: 0.7720 (t0) REVERT: C 28 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7658 (ttmm) REVERT: C 87 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7511 (p) REVERT: C 100 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7929 (ttp-170) REVERT: D 77 SER cc_start: 0.8348 (t) cc_final: 0.8037 (p) REVERT: D 92 ASP cc_start: 0.8369 (t0) cc_final: 0.7941 (t0) REVERT: D 93 SER cc_start: 0.8162 (p) cc_final: 0.7919 (p) REVERT: D 95 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7462 (pp) REVERT: E 147 ASN cc_start: 0.8147 (m-40) cc_final: 0.7827 (m110) REVERT: E 210 ARG cc_start: 0.8340 (ptp90) cc_final: 0.8032 (ptp-110) REVERT: E 213 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: E 431 LYS cc_start: 0.7811 (tppt) cc_final: 0.7457 (tppt) REVERT: F 87 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7585 (p) REVERT: G 61 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7849 (ptp90) REVERT: G 77 SER cc_start: 0.8488 (t) cc_final: 0.7974 (p) REVERT: G 92 ASP cc_start: 0.8417 (t0) cc_final: 0.8012 (t0) REVERT: H 147 ASN cc_start: 0.8149 (m-40) cc_final: 0.7775 (m110) REVERT: H 210 ARG cc_start: 0.8461 (ptp90) cc_final: 0.8168 (ptp-110) REVERT: H 247 SER cc_start: 0.8343 (m) cc_final: 0.8080 (p) REVERT: H 392 THR cc_start: 0.8522 (m) cc_final: 0.8144 (t) REVERT: I 63 VAL cc_start: 0.8473 (m) cc_final: 0.8136 (t) REVERT: J 61 ARG cc_start: 0.8360 (ptp90) cc_final: 0.7896 (ptp90) REVERT: J 77 SER cc_start: 0.8379 (t) cc_final: 0.7836 (p) REVERT: J 92 ASP cc_start: 0.8476 (t0) cc_final: 0.8065 (t0) outliers start: 82 outliers final: 59 residues processed: 478 average time/residue: 0.5071 time to fit residues: 277.7319 Evaluate side-chains 499 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 430 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE 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 48 ILE 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 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 389 LYS Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 442 SER 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 199 ASN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 226 GLN 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 312 ILE Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 417 CYS 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 222 ILE Chi-restraints excluded: chain H residue 249 LYS Chi-restraints excluded: chain H residue 369 THR 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 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 203 optimal weight: 0.0070 chunk 67 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 217 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 226 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 136 GLN E 199 ASN E 226 GLN H 199 ASN H 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094171 restraints weight = 28063.752| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.94 r_work: 0.2982 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20032 Z= 0.113 Angle : 0.570 7.251 27248 Z= 0.297 Chirality : 0.045 0.153 2952 Planarity : 0.004 0.047 3476 Dihedral : 4.804 20.091 3048 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.85 % Favored : 93.98 % Rotamer: Outliers : 3.25 % Allowed : 18.16 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.16), residues: 2460 helix: 0.28 (1.09), residues: 24 sheet: 0.46 (0.18), residues: 932 loop : -2.24 (0.13), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.025 0.001 TYR N 94 PHE 0.016 0.002 PHE A 410 TRP 0.020 0.001 TRP M 36 HIS 0.003 0.001 HIS H 144 Details of bonding type rmsd covalent geometry : bond 0.00263 (19972) covalent geometry : angle 0.56105 (27112) SS BOND : bond 0.00381 ( 44) SS BOND : angle 1.19688 ( 88) hydrogen bonds : bond 0.03396 ( 552) hydrogen bonds : angle 5.32891 ( 1620) link_NAG-ASN : bond 0.00200 ( 16) link_NAG-ASN : angle 1.95862 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6392.26 seconds wall clock time: 109 minutes 38.74 seconds (6578.74 seconds total)