Starting phenix.real_space_refine on Thu Aug 6 05:49:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13jv_77099/08_2026/13jv_77099.cif Found real_map, /net/cci-nas-00/data/ceres_data/13jv_77099/08_2026/13jv_77099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13jv_77099/08_2026/13jv_77099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13jv_77099/08_2026/13jv_77099.map" model { file = "/net/cci-nas-00/data/ceres_data/13jv_77099/08_2026/13jv_77099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13jv_77099/08_2026/13jv_77099.cif" } resolution = 3.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 72 5.16 5 C 8543 2.51 5 N 2265 2.21 5 O 2601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13490 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3784 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3784 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3784 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 588 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 588 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 588 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 67 Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Time building chain proxies: 3.64, per 1000 atoms: 0.27 Number of scatterers: 13490 At special positions: 0 Unit cell: (202.663, 107.423, 95.2407, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 9 15.00 O 2601 8.00 N 2265 7.00 C 8543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 305 " - pdb=" SG CYS C 336 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG G 1 " - " ASN A 154 " " NAG H 1 " - " ASN B 154 " " NAG I 1 " - " ASN C 154 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 651.5 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3108 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 26 sheets defined 32.6% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.048A pdb=" N SER A 86 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.578A pdb=" N GLN A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 235 through 238 removed outlier: 3.647A pdb=" N THR A 238 " --> pdb=" O ASN A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 402 through 422 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 433 through 455 Processing helix chain 'A' and resid 458 through 475 Processing helix chain 'A' and resid 478 through 498 Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.786A pdb=" N SER B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 150 through 153 removed outlier: 3.914A pdb=" N GLY B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 153' Processing helix chain 'B' and resid 154 through 161 Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 235 through 238 removed outlier: 3.563A pdb=" N THR B 238 " --> pdb=" O ASN B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 402 through 422 Processing helix chain 'B' and resid 423 through 428 removed outlier: 3.528A pdb=" N PHE B 428 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.728A pdb=" N VAL B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 475 removed outlier: 3.654A pdb=" N GLN B 475 " --> pdb=" O TRP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 498 Processing helix chain 'C' and resid 82 through 87 removed outlier: 4.022A pdb=" N SER C 86 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.860A pdb=" N ILE C 135 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 removed outlier: 3.839A pdb=" N GLY C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 153' Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'C' and resid 235 through 238 removed outlier: 4.144A pdb=" N THR C 238 " --> pdb=" O ASN C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 402 through 422 Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.820A pdb=" N TRP C 426 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 428 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 455 removed outlier: 3.767A pdb=" N GLY C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 475 removed outlier: 3.695A pdb=" N GLN C 475 " --> pdb=" O TRP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 498 removed outlier: 3.922A pdb=" N THR C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 486 " --> pdb=" O SER C 482 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 488 " --> pdb=" O THR C 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 28 through 39 removed outlier: 3.775A pdb=" N GLU D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 4.299A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 74 Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 1 through 5 removed outlier: 3.914A pdb=" N VAL E 4 " --> pdb=" O SER E 1 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 41 through 54 removed outlier: 3.824A pdb=" N VAL E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 74 Proline residue: E 72 - end of helix Processing helix chain 'F' and resid 20 through 26 Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 40 through 54 removed outlier: 4.244A pdb=" N LEU F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 75 removed outlier: 3.757A pdb=" N ALA F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.361A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU A 138 " --> pdb=" O MET A 46 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N MET A 48 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS A 136 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.361A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 26 removed outlier: 3.556A pdb=" N ARG A 289 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 187 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 99 removed outlier: 5.007A pdb=" N GLY A 111 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG A 73 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 113 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 71 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A 115 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER A 69 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA A 117 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR A 67 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 119 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU A 65 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS A 121 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 63 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN A 123 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 57 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR A 129 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR A 55 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 99 removed outlier: 4.464A pdb=" N SER A 210 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 270 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 303 through 304 removed outlier: 6.815A pdb=" N GLY A 303 " --> pdb=" O ARG A 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 309 through 317 removed outlier: 6.334A pdb=" N SER A 312 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLN A 328 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN A 314 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU A 326 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 354 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 340 through 343 Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.386A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE B 43 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE B 142 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL B 45 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA B 140 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 47 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.386A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 26 removed outlier: 3.962A pdb=" N ARG B 289 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR B 187 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP B 293 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR B 185 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 90 through 99 removed outlier: 9.200A pdb=" N GLY B 111 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA B 72 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ILE B 113 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N THR B 70 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N THR B 115 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LEU B 68 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA B 117 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP B 66 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE B 119 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR B 64 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N CYS B 121 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLU B 62 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASN B 123 " --> pdb=" O CYS B 60 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N CYS B 60 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA B 125 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU B 58 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY B 127 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 54 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 99 removed outlier: 4.418A pdb=" N SER B 210 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 270 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AB7, first strand: chain 'B' and resid 309 through 317 removed outlier: 7.008A pdb=" N GLU B 326 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN B 314 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 324 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN B 369 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 354 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 340 through 343 removed outlier: 3.549A pdb=" N GLY B 380 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.467A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE C 43 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE C 142 " --> pdb=" O PHE C 43 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL C 45 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 140 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 47 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.467A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET C 48 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.831A pdb=" N THR C 187 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.661A pdb=" N ALA C 54 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY C 127 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU C 58 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C 125 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER C 210 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 270 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 63 through 72 removed outlier: 4.458A pdb=" N LEU C 68 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS C 116 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 70 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 114 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA C 72 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N SER C 112 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 240 through 242 Processing sheet with id=AC6, first strand: chain 'C' and resid 303 through 304 removed outlier: 7.080A pdb=" N GLY C 303 " --> pdb=" O ARG C 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.213A pdb=" N GLU C 326 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN C 314 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 324 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 369 " --> pdb=" O TYR C 329 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 340 through 343 608 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.48 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: 2337 1.33 - 1.45: 3643 1.45 - 1.57: 7660 1.57 - 1.69: 18 1.69 - 1.81: 108 Bond restraints: 13766 Sorted by residual: bond pdb=" CA VAL C 499 " pdb=" CB VAL C 499 " ideal model delta sigma weight residual 1.540 1.564 -0.024 2.70e-02 1.37e+03 7.75e-01 bond pdb=" N VAL C 499 " pdb=" CA VAL C 499 " ideal model delta sigma weight residual 1.458 1.472 -0.014 1.90e-02 2.77e+03 5.81e-01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.533 -0.014 2.00e-02 2.50e+03 4.69e-01 bond pdb=" C1 NAG H 2 " pdb=" C2 NAG H 2 " ideal model delta sigma weight residual 1.532 1.545 -0.013 2.00e-02 2.50e+03 4.16e-01 bond pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sigma weight residual 1.410 1.423 -0.013 2.00e-02 2.50e+03 3.92e-01 ... (remaining 13761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18414 1.31 - 2.63: 185 2.63 - 3.94: 61 3.94 - 5.25: 12 5.25 - 6.57: 2 Bond angle restraints: 18674 Sorted by residual: angle pdb=" C SER C 498 " pdb=" N VAL C 499 " pdb=" CA VAL C 499 " ideal model delta sigma weight residual 121.70 125.94 -4.24 1.80e+00 3.09e-01 5.56e+00 angle pdb=" CA GLU C 37 " pdb=" CB GLU C 37 " pdb=" CG GLU C 37 " ideal model delta sigma weight residual 114.10 118.18 -4.08 2.00e+00 2.50e-01 4.17e+00 angle pdb=" CA LEU C 281 " pdb=" CB LEU C 281 " pdb=" CG LEU C 281 " ideal model delta sigma weight residual 116.30 122.87 -6.57 3.50e+00 8.16e-02 3.52e+00 angle pdb=" CA VAL C 499 " pdb=" C VAL C 499 " pdb=" O VAL C 499 " ideal model delta sigma weight residual 120.80 123.93 -3.13 1.70e+00 3.46e-01 3.39e+00 angle pdb=" CB PRO B 271 " pdb=" CG PRO B 271 " pdb=" CD PRO B 271 " ideal model delta sigma weight residual 106.10 100.46 5.64 3.20e+00 9.77e-02 3.11e+00 ... (remaining 18669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 7780 23.96 - 47.92: 430 47.92 - 71.87: 51 71.87 - 95.83: 10 95.83 - 119.79: 2 Dihedral angle restraints: 8273 sinusoidal: 3407 harmonic: 4866 Sorted by residual: dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual 93.00 157.67 -64.67 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 121 " pdb=" CB CYS B 121 " ideal model delta sinusoidal sigma weight residual -86.00 -143.29 57.29 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " pdb=" SG CYS C 121 " pdb=" CB CYS C 121 " ideal model delta sinusoidal sigma weight residual -86.00 -142.32 56.32 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 8270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1291 0.026 - 0.052: 531 0.052 - 0.078: 173 0.078 - 0.103: 103 0.103 - 0.129: 65 Chirality restraints: 2163 Sorted by residual: chirality pdb=" CB THR B 231 " pdb=" CA THR B 231 " pdb=" OG1 THR B 231 " pdb=" CG2 THR B 231 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE A 270 " pdb=" N ILE A 270 " pdb=" C ILE A 270 " pdb=" CB ILE A 270 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" C4 NAG H 2 " pdb=" C3 NAG H 2 " pdb=" C5 NAG H 2 " pdb=" O4 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.41 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 2160 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 71 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO D 72 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 72 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 72 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 71 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO E 72 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 338 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 339 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.018 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4067 2.83 - 3.35: 11269 3.35 - 3.87: 20996 3.87 - 4.38: 23356 4.38 - 4.90: 43708 Nonbonded interactions: 103396 Sorted by model distance: nonbonded pdb=" OG1 THR C 40 " pdb=" O VAL C 356 " model vdw 2.313 3.040 nonbonded pdb=" ND2 ASN A 314 " pdb=" OE2 GLU C 133 " model vdw 2.331 3.120 nonbonded pdb=" ND2 ASN A 197 " pdb=" OD2 ASP A 200 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASP A 220 " pdb=" NH2 ARG E 38 " model vdw 2.346 3.120 nonbonded pdb=" O SER C 194 " pdb=" OG SER C 194 " model vdw 2.349 3.040 ... (remaining 103391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 601 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or n \ ame C3 or name C31 or name C32 or name O11 or name O12 or name O13 or name O14 o \ r name O21 or name O22 or name O31 or name O32 or name P )) or (resid 603 and (n \ ame N or name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or n \ ame C23 or name C24 or name C3 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name C \ 3B or name C3C or name C3D or name C3E or name C3F or name O11 or name O12 or na \ me O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P ))) \ ) selection = (chain 'B' and (resid 1 through 499 or (resid 601 and (name N or name C1 or name \ C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C3 or name C31 or name C32 or name O11 or name O12 or name O13 o \ r name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resi \ d 602 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C3 or name C31 or name C32 or name O11 o \ r name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O \ 32 or name P )) or (resid 603 and (name N or name C1 or name C11 or name C12 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name C39 or name C3A or name C3B or name C3C or name C3D or name C3E or na \ me C3F or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 1 through 499 or (resid 601 and (name N or name C1 or name \ C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C3 or name C31 or name C32 or name O11 or name O12 or name O13 o \ r name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resi \ d 602 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C3 or name C31 or name C32 or name O11 o \ r name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O \ 32 or name P )) or (resid 603 and (name N or name C1 or name C11 or name C12 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name C39 or name C3A or name C3B or name C3C or name C3D or name C3E or na \ me C3F or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r name O31 or name O32 or name P )))) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.280 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.002 0.024 13788 Z= 0.074 Angle : 0.413 6.566 18727 Z= 0.201 Chirality : 0.039 0.129 2163 Planarity : 0.003 0.039 2325 Dihedral : 13.973 119.788 5126 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1710 helix: 1.52 (0.25), residues: 489 sheet: 0.50 (0.23), residues: 555 loop : -0.94 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.008 0.001 TYR E 42 PHE 0.022 0.001 PHE D 63 TRP 0.009 0.001 TRP B 471 HIS 0.003 0.000 HIS C 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00155 / 0.07 (13766) covalent geometry : angle 0.40693 / 0.20 (18674) SS BOND : bond 0.00134 / 0.06 ( 13) SS BOND : angle 0.40049 / 0.24 ( 26) hydrogen bonds : bond 0.18823 / 12.61 ( 576) hydrogen bonds : angle 7.60030 / 4.99 ( 1713) link_BETA1-4 : bond 0.00840 / 0.42 ( 6) link_BETA1-4 : angle 2.16007 / 1.21 ( 18) link_NAG-ASN : bond 0.00228 / 0.11 ( 3) link_NAG-ASN : angle 1.03243 / 0.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.502 Fit side-chains REVERT: A 22 ASP cc_start: 0.8093 (t0) cc_final: 0.7870 (t0) REVERT: B 22 ASP cc_start: 0.8816 (m-30) cc_final: 0.8340 (m-30) REVERT: B 413 LYS cc_start: 0.8450 (tppt) cc_final: 0.8237 (tppt) REVERT: B 451 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7848 (ttm110) REVERT: C 277 SER cc_start: 0.8644 (m) cc_final: 0.8307 (p) REVERT: D 51 TRP cc_start: 0.6323 (t-100) cc_final: 0.6069 (m-90) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1120 time to fit residues: 47.2128 Evaluate side-chains 202 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN B 333 ASN B 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.105130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.086321 restraints weight = 17374.255| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.53 r_work: 0.2659 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 13788 Z= 0.305 Angle : 0.653 9.314 18727 Z= 0.335 Chirality : 0.048 0.182 2163 Planarity : 0.005 0.044 2325 Dihedral : 10.468 130.298 2249 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.26 % Allowed : 8.47 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1710 helix: 1.07 (0.24), residues: 495 sheet: 0.03 (0.22), residues: 543 loop : -1.17 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 193 TYR 0.019 0.002 TYR B 155 PHE 0.022 0.002 PHE D 63 TRP 0.016 0.002 TRP B 233 HIS 0.010 0.002 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.31 (13766) covalent geometry : angle 0.64606 / 0.33 (18674) SS BOND : bond 0.00482 / 0.21 ( 13) SS BOND : angle 1.30360 / 0.83 ( 26) hydrogen bonds : bond 0.04847 / 3.23 ( 576) hydrogen bonds : angle 5.38749 / 3.59 ( 1713) link_BETA1-4 : bond 0.00536 / 0.27 ( 6) link_BETA1-4 : angle 2.55523 / 1.45 ( 18) link_NAG-ASN : bond 0.00351 / 0.18 ( 3) link_NAG-ASN : angle 1.54034 / 0.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.507 Fit side-chains REVERT: A 22 ASP cc_start: 0.8193 (t0) cc_final: 0.7946 (t0) REVERT: B 413 LYS cc_start: 0.8707 (tppt) cc_final: 0.8426 (tppt) REVERT: C 201 TYR cc_start: 0.9340 (m-80) cc_final: 0.8893 (m-80) REVERT: C 277 SER cc_start: 0.8637 (m) cc_final: 0.8287 (p) REVERT: D 51 TRP cc_start: 0.6834 (t-100) cc_final: 0.6558 (m-90) REVERT: E 3 SER cc_start: 0.9125 (p) cc_final: 0.8735 (m) REVERT: E 66 MET cc_start: 0.8680 (mtm) cc_final: 0.8462 (mtm) REVERT: F 52 MET cc_start: 0.8429 (ttp) cc_final: 0.8046 (ttm) outliers start: 32 outliers final: 26 residues processed: 229 average time/residue: 0.1107 time to fit residues: 37.6879 Evaluate side-chains 218 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN E 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.105033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.086146 restraints weight = 17383.747| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.55 r_work: 0.2661 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13788 Z= 0.220 Angle : 0.568 11.081 18727 Z= 0.292 Chirality : 0.044 0.162 2163 Planarity : 0.004 0.041 2325 Dihedral : 10.548 136.031 2249 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.47 % Allowed : 11.16 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1710 helix: 1.20 (0.24), residues: 477 sheet: -0.13 (0.21), residues: 537 loop : -1.08 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 451 TYR 0.016 0.002 TYR D 74 PHE 0.017 0.001 PHE C 119 TRP 0.014 0.002 TRP B 233 HIS 0.007 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.22 (13766) covalent geometry : angle 0.55972 / 0.29 (18674) SS BOND : bond 0.00536 / 0.22 ( 13) SS BOND : angle 1.46981 / 0.98 ( 26) hydrogen bonds : bond 0.04286 / 2.85 ( 576) hydrogen bonds : angle 5.08950 / 3.40 ( 1713) link_BETA1-4 : bond 0.00769 / 0.39 ( 6) link_BETA1-4 : angle 2.53731 / 1.43 ( 18) link_NAG-ASN : bond 0.00310 / 0.16 ( 3) link_NAG-ASN : angle 1.50934 / 0.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.529 Fit side-chains REVERT: A 22 ASP cc_start: 0.8161 (t0) cc_final: 0.7880 (t0) REVERT: B 413 LYS cc_start: 0.8709 (tppt) cc_final: 0.8383 (tppt) REVERT: C 277 SER cc_start: 0.8604 (m) cc_final: 0.8254 (p) REVERT: D 51 TRP cc_start: 0.6685 (t-100) cc_final: 0.6443 (m-90) REVERT: E 3 SER cc_start: 0.9130 (p) cc_final: 0.8741 (m) REVERT: F 52 MET cc_start: 0.8467 (ttp) cc_final: 0.8040 (ttm) outliers start: 35 outliers final: 29 residues processed: 215 average time/residue: 0.1090 time to fit residues: 35.3428 Evaluate side-chains 211 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN B 81 HIS C 179 ASN E 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.104187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.085732 restraints weight = 17343.439| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.48 r_work: 0.2650 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13788 Z= 0.229 Angle : 0.571 10.556 18727 Z= 0.293 Chirality : 0.044 0.161 2163 Planarity : 0.004 0.038 2325 Dihedral : 10.763 140.556 2249 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.97 % Allowed : 12.36 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1710 helix: 1.32 (0.24), residues: 459 sheet: -0.30 (0.21), residues: 543 loop : -0.95 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 57 TYR 0.018 0.002 TYR D 74 PHE 0.017 0.002 PHE C 119 TRP 0.014 0.002 TRP B 233 HIS 0.007 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 (13766) covalent geometry : angle 0.56266 / 0.29 (18674) SS BOND : bond 0.00620 / 0.24 ( 13) SS BOND : angle 1.48377 / 1.03 ( 26) hydrogen bonds : bond 0.04235 / 2.81 ( 576) hydrogen bonds : angle 4.92679 / 3.30 ( 1713) link_BETA1-4 : bond 0.00670 / 0.34 ( 6) link_BETA1-4 : angle 2.49986 / 1.42 ( 18) link_NAG-ASN : bond 0.00331 / 0.17 ( 3) link_NAG-ASN : angle 1.61238 / 0.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.435 Fit side-chains REVERT: A 22 ASP cc_start: 0.8207 (t0) cc_final: 0.7824 (t0) REVERT: A 324 ILE cc_start: 0.8996 (mt) cc_final: 0.8752 (tp) REVERT: B 413 LYS cc_start: 0.8667 (tppt) cc_final: 0.8367 (tppt) REVERT: C 277 SER cc_start: 0.8629 (m) cc_final: 0.8306 (p) REVERT: C 292 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8688 (mt) REVERT: D 51 TRP cc_start: 0.6760 (t-100) cc_final: 0.6445 (m-90) REVERT: E 3 SER cc_start: 0.9106 (p) cc_final: 0.8720 (m) REVERT: F 52 MET cc_start: 0.8675 (ttp) cc_final: 0.8299 (ttm) outliers start: 42 outliers final: 34 residues processed: 225 average time/residue: 0.1124 time to fit residues: 37.9164 Evaluate side-chains 223 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.087399 restraints weight = 17397.453| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.54 r_work: 0.2681 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13788 Z= 0.119 Angle : 0.487 9.364 18727 Z= 0.250 Chirality : 0.041 0.145 2163 Planarity : 0.003 0.034 2325 Dihedral : 10.423 138.494 2249 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.47 % Allowed : 13.49 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1710 helix: 1.28 (0.24), residues: 480 sheet: -0.21 (0.21), residues: 543 loop : -0.92 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 451 TYR 0.013 0.001 TYR B 155 PHE 0.014 0.001 PHE C 119 TRP 0.013 0.001 TRP B 233 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13766) covalent geometry : angle 0.47889 / 0.25 (18674) SS BOND : bond 0.00568 / 0.20 ( 13) SS BOND : angle 1.15149 / 0.80 ( 26) hydrogen bonds : bond 0.03462 / 2.29 ( 576) hydrogen bonds : angle 4.73507 / 3.17 ( 1713) link_BETA1-4 : bond 0.00683 / 0.35 ( 6) link_BETA1-4 : angle 2.45708 / 1.38 ( 18) link_NAG-ASN : bond 0.00254 / 0.13 ( 3) link_NAG-ASN : angle 1.33575 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.513 Fit side-chains REVERT: A 22 ASP cc_start: 0.8211 (t0) cc_final: 0.7839 (t0) REVERT: A 324 ILE cc_start: 0.8930 (mt) cc_final: 0.8683 (tp) REVERT: B 88 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8318 (tp) REVERT: B 413 LYS cc_start: 0.8579 (tppt) cc_final: 0.8263 (tppt) REVERT: C 138 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: C 277 SER cc_start: 0.8597 (m) cc_final: 0.8258 (p) REVERT: D 51 TRP cc_start: 0.6760 (t-100) cc_final: 0.6348 (m-90) REVERT: E 3 SER cc_start: 0.9118 (p) cc_final: 0.8721 (m) REVERT: F 52 MET cc_start: 0.8671 (ttp) cc_final: 0.8319 (ttm) outliers start: 35 outliers final: 30 residues processed: 220 average time/residue: 0.1100 time to fit residues: 36.3555 Evaluate side-chains 218 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.105263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.086647 restraints weight = 17294.919| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.53 r_work: 0.2668 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13788 Z= 0.161 Angle : 0.510 9.368 18727 Z= 0.262 Chirality : 0.042 0.155 2163 Planarity : 0.004 0.033 2325 Dihedral : 10.457 138.559 2249 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.90 % Allowed : 13.28 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1710 helix: 1.28 (0.24), residues: 480 sheet: -0.23 (0.21), residues: 543 loop : -0.89 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 451 TYR 0.015 0.001 TYR B 155 PHE 0.015 0.001 PHE C 119 TRP 0.012 0.001 TRP B 233 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (13766) covalent geometry : angle 0.50252 / 0.26 (18674) SS BOND : bond 0.00518 / 0.19 ( 13) SS BOND : angle 1.19375 / 0.84 ( 26) hydrogen bonds : bond 0.03653 / 2.42 ( 576) hydrogen bonds : angle 4.68827 / 3.14 ( 1713) link_BETA1-4 : bond 0.00690 / 0.35 ( 6) link_BETA1-4 : angle 2.39998 / 1.37 ( 18) link_NAG-ASN : bond 0.00286 / 0.14 ( 3) link_NAG-ASN : angle 1.40606 / 0.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.514 Fit side-chains REVERT: A 22 ASP cc_start: 0.8174 (t0) cc_final: 0.7910 (t0) REVERT: A 324 ILE cc_start: 0.8900 (mt) cc_final: 0.8695 (tp) REVERT: A 410 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8791 (p) REVERT: B 413 LYS cc_start: 0.8544 (tppt) cc_final: 0.8234 (tppt) REVERT: B 471 TRP cc_start: 0.8643 (t-100) cc_final: 0.8438 (t-100) REVERT: C 138 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: C 277 SER cc_start: 0.8459 (m) cc_final: 0.8154 (p) REVERT: E 3 SER cc_start: 0.9116 (p) cc_final: 0.8743 (m) REVERT: F 52 MET cc_start: 0.8672 (ttp) cc_final: 0.8331 (ttm) outliers start: 41 outliers final: 37 residues processed: 215 average time/residue: 0.1059 time to fit residues: 34.4807 Evaluate side-chains 224 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 3 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.104853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.086264 restraints weight = 17283.454| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.53 r_work: 0.2662 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13788 Z= 0.176 Angle : 0.522 9.103 18727 Z= 0.268 Chirality : 0.043 0.165 2163 Planarity : 0.004 0.034 2325 Dihedral : 10.519 140.159 2249 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.60 % Allowed : 13.21 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1710 helix: 1.25 (0.24), residues: 480 sheet: -0.22 (0.21), residues: 537 loop : -0.90 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.018 0.002 TYR B 155 PHE 0.015 0.001 PHE C 119 TRP 0.014 0.001 TRP B 233 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (13766) covalent geometry : angle 0.51449 / 0.27 (18674) SS BOND : bond 0.00534 / 0.20 ( 13) SS BOND : angle 1.25061 / 0.87 ( 26) hydrogen bonds : bond 0.03780 / 2.50 ( 576) hydrogen bonds : angle 4.67830 / 3.15 ( 1713) link_BETA1-4 : bond 0.00678 / 0.35 ( 6) link_BETA1-4 : angle 2.34882 / 1.34 ( 18) link_NAG-ASN : bond 0.00299 / 0.15 ( 3) link_NAG-ASN : angle 1.46994 / 0.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.503 Fit side-chains REVERT: A 22 ASP cc_start: 0.8199 (t0) cc_final: 0.7922 (t0) REVERT: A 324 ILE cc_start: 0.8909 (mt) cc_final: 0.8701 (tp) REVERT: A 410 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 413 LYS cc_start: 0.8541 (tppt) cc_final: 0.8235 (tppt) REVERT: B 471 TRP cc_start: 0.8660 (t-100) cc_final: 0.8453 (t-100) REVERT: C 138 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: C 277 SER cc_start: 0.8505 (m) cc_final: 0.8208 (p) REVERT: C 292 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8653 (mt) REVERT: E 3 SER cc_start: 0.9120 (p) cc_final: 0.8747 (m) REVERT: F 52 MET cc_start: 0.8662 (ttp) cc_final: 0.8331 (ttm) outliers start: 51 outliers final: 43 residues processed: 228 average time/residue: 0.1077 time to fit residues: 37.2643 Evaluate side-chains 233 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 3 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.104848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.086280 restraints weight = 17256.614| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.52 r_work: 0.2661 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13788 Z= 0.172 Angle : 0.519 9.572 18727 Z= 0.266 Chirality : 0.043 0.176 2163 Planarity : 0.004 0.034 2325 Dihedral : 10.537 141.408 2249 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.25 % Allowed : 13.63 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1710 helix: 1.24 (0.24), residues: 480 sheet: -0.21 (0.21), residues: 537 loop : -0.87 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.017 0.002 TYR B 155 PHE 0.015 0.001 PHE C 119 TRP 0.013 0.001 TRP B 233 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (13766) covalent geometry : angle 0.51198 / 0.26 (18674) SS BOND : bond 0.00562 / 0.21 ( 13) SS BOND : angle 1.22441 / 0.85 ( 26) hydrogen bonds : bond 0.03755 / 2.48 ( 576) hydrogen bonds : angle 4.65650 / 3.14 ( 1713) link_BETA1-4 : bond 0.00707 / 0.36 ( 6) link_BETA1-4 : angle 2.31976 / 1.33 ( 18) link_NAG-ASN : bond 0.00281 / 0.14 ( 3) link_NAG-ASN : angle 1.47311 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.539 Fit side-chains REVERT: A 22 ASP cc_start: 0.8186 (t0) cc_final: 0.7793 (t0) REVERT: A 410 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8795 (p) REVERT: B 132 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8341 (mtp180) REVERT: B 413 LYS cc_start: 0.8525 (tppt) cc_final: 0.8218 (tppt) REVERT: B 471 TRP cc_start: 0.8647 (t-100) cc_final: 0.8446 (t-100) REVERT: C 138 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: C 277 SER cc_start: 0.8496 (m) cc_final: 0.8202 (p) REVERT: C 292 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8633 (mt) REVERT: E 3 SER cc_start: 0.9119 (p) cc_final: 0.8760 (m) REVERT: F 52 MET cc_start: 0.8656 (ttp) cc_final: 0.8336 (ttm) outliers start: 46 outliers final: 42 residues processed: 220 average time/residue: 0.1070 time to fit residues: 35.6195 Evaluate side-chains 230 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 3 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN E 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.102280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.083665 restraints weight = 17501.066| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.53 r_work: 0.2623 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13788 Z= 0.325 Angle : 0.648 10.666 18727 Z= 0.332 Chirality : 0.048 0.297 2163 Planarity : 0.005 0.049 2325 Dihedral : 11.152 149.140 2249 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 3.53 % Allowed : 13.49 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1710 helix: 0.93 (0.24), residues: 480 sheet: -0.42 (0.21), residues: 537 loop : -1.07 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 236 TYR 0.027 0.002 TYR D 74 PHE 0.021 0.002 PHE C 119 TRP 0.015 0.002 TRP B 233 HIS 0.008 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.33 (13766) covalent geometry : angle 0.64050 / 0.33 (18674) SS BOND : bond 0.00712 / 0.28 ( 13) SS BOND : angle 1.58964 / 1.16 ( 26) hydrogen bonds : bond 0.04802 / 3.17 ( 576) hydrogen bonds : angle 4.88853 / 3.30 ( 1713) link_BETA1-4 : bond 0.00736 / 0.37 ( 6) link_BETA1-4 : angle 2.38619 / 1.39 ( 18) link_NAG-ASN : bond 0.00426 / 0.22 ( 3) link_NAG-ASN : angle 2.06034 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.508 Fit side-chains REVERT: A 22 ASP cc_start: 0.8229 (t0) cc_final: 0.7929 (t0) REVERT: A 410 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8809 (p) REVERT: B 132 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8136 (mtp180) REVERT: B 413 LYS cc_start: 0.8635 (tppt) cc_final: 0.8308 (tppt) REVERT: C 277 SER cc_start: 0.8688 (m) cc_final: 0.8353 (p) REVERT: C 292 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8693 (mt) REVERT: E 3 SER cc_start: 0.9075 (p) cc_final: 0.8695 (m) REVERT: F 52 MET cc_start: 0.8622 (ttp) cc_final: 0.8314 (ttm) outliers start: 50 outliers final: 39 residues processed: 217 average time/residue: 0.1076 time to fit residues: 35.1960 Evaluate side-chains 224 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 3 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 125 optimal weight: 0.0980 chunk 106 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 HIS E 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.105716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.087131 restraints weight = 17287.825| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.53 r_work: 0.2682 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13788 Z= 0.113 Angle : 0.491 8.852 18727 Z= 0.252 Chirality : 0.042 0.173 2163 Planarity : 0.003 0.034 2325 Dihedral : 10.631 146.119 2249 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.33 % Allowed : 14.69 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1710 helix: 1.24 (0.24), residues: 480 sheet: -0.24 (0.21), residues: 537 loop : -0.84 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 451 TYR 0.013 0.001 TYR B 155 PHE 0.013 0.001 PHE C 119 TRP 0.016 0.001 TRP B 233 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (13766) covalent geometry : angle 0.48373 / 0.25 (18674) SS BOND : bond 0.00461 / 0.17 ( 13) SS BOND : angle 1.09286 / 0.74 ( 26) hydrogen bonds : bond 0.03450 / 2.29 ( 576) hydrogen bonds : angle 4.62108 / 3.13 ( 1713) link_BETA1-4 : bond 0.00768 / 0.39 ( 6) link_BETA1-4 : angle 2.35383 / 1.35 ( 18) link_NAG-ASN : bond 0.00211 / 0.10 ( 3) link_NAG-ASN : angle 1.44213 / 0.89 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.438 Fit side-chains REVERT: A 22 ASP cc_start: 0.8168 (t0) cc_final: 0.7798 (t0) REVERT: B 132 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8019 (mtp180) REVERT: B 413 LYS cc_start: 0.8571 (tppt) cc_final: 0.8260 (tppt) REVERT: C 56 VAL cc_start: 0.9156 (t) cc_final: 0.8797 (m) REVERT: C 235 ASN cc_start: 0.8938 (t0) cc_final: 0.8541 (t0) REVERT: C 277 SER cc_start: 0.8634 (m) cc_final: 0.8307 (p) REVERT: C 292 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8621 (mt) REVERT: E 3 SER cc_start: 0.9110 (p) cc_final: 0.8749 (m) REVERT: F 52 MET cc_start: 0.8647 (ttp) cc_final: 0.8362 (ttm) outliers start: 33 outliers final: 28 residues processed: 221 average time/residue: 0.1040 time to fit residues: 34.8938 Evaluate side-chains 218 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.105133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.086852 restraints weight = 17318.903| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.47 r_work: 0.2668 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13788 Z= 0.149 Angle : 0.511 8.993 18727 Z= 0.262 Chirality : 0.042 0.167 2163 Planarity : 0.003 0.034 2325 Dihedral : 10.606 146.012 2249 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.47 % Allowed : 14.69 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1710 helix: 1.26 (0.24), residues: 480 sheet: -0.23 (0.21), residues: 537 loop : -0.81 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 451 TYR 0.016 0.001 TYR B 155 PHE 0.014 0.001 PHE C 119 TRP 0.014 0.001 TRP B 233 HIS 0.005 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (13766) covalent geometry : angle 0.50358 / 0.26 (18674) SS BOND : bond 0.00505 / 0.19 ( 13) SS BOND : angle 1.16026 / 0.80 ( 26) hydrogen bonds : bond 0.03605 / 2.38 ( 576) hydrogen bonds : angle 4.59361 / 3.10 ( 1713) link_BETA1-4 : bond 0.00730 / 0.37 ( 6) link_BETA1-4 : angle 2.28224 / 1.32 ( 18) link_NAG-ASN : bond 0.00273 / 0.14 ( 3) link_NAG-ASN : angle 1.49398 / 0.91 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3399.17 seconds wall clock time: 59 minutes 10.46 seconds (3550.46 seconds total)