Starting phenix.real_space_refine on Fri Jul 3 22:25:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cc6_16555/07_2026/8cc6_16555.cif" } resolution = 3.2 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= 0.000 sd= 0.065 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 S 45 5.16 5 Cl 5 4.86 5 C 10965 2.51 5 N 2690 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16640 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "C" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "D" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "E" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'U9L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.12, per 1000 atoms: 0.25 Number of scatterers: 16640 At special positions: 0 Unit cell: (95.035, 96.18, 168.315, 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) Cl 5 17.00 S 45 16.00 O 2935 8.00 N 2690 7.00 C 10965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 501 " - " ASN D 82 " " NAG E1002 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN B 164 " " NAG I 1 " - " ASN B 148 " " NAG J 1 " - " ASN C 164 " " NAG K 1 " - " ASN C 148 " " NAG L 1 " - " ASN D 164 " " NAG M 1 " - " ASN D 148 " " NAG N 1 " - " ASN E 164 " " NAG O 1 " - " ASN E 148 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 973.4 milliseconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3790 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 48.6% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 243 removed outlier: 3.874A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.826A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 5.976A pdb=" N ASP A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY A 249 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 270 Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.912A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 4.853A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 460 removed outlier: 3.614A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.296A pdb=" N ASP B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.859A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 3.864A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 6.016A pdb=" N ASP B 247 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 270 Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.884A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 4.800A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 460 removed outlier: 3.591A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 243 removed outlier: 4.897A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.884A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 removed outlier: 6.008A pdb=" N ASP C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 249 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 270 Processing helix chain 'C' and resid 282 through 309 removed outlier: 3.932A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 4.826A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 460 removed outlier: 3.603A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 76 through 81 removed outlier: 4.278A pdb=" N ASP D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 243 removed outlier: 4.880A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.802A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 removed outlier: 5.964A pdb=" N ASP D 247 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 270 Processing helix chain 'D' and resid 282 through 309 removed outlier: 3.896A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 4.851A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 460 removed outlier: 3.661A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 223 through 243 removed outlier: 3.843A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix removed outlier: 3.828A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 249 removed outlier: 5.990A pdb=" N ASP E 247 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY E 249 " --> pdb=" O PRO E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 270 Processing helix chain 'E' and resid 282 through 309 removed outlier: 3.901A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 4.845A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 460 removed outlier: 3.619A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.803A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.803A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.401A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.852A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.852A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.503A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.743A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN C 130 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 106 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.743A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.442A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.782A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.782A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.411A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR D 207 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU D 198 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU D 209 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE D 196 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.759A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.759A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.449A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5055 1.34 - 1.46: 3561 1.46 - 1.57: 8414 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 17105 Sorted by residual: bond pdb=" C20 U9L B 502 " pdb=" N21 U9L B 502 " ideal model delta sigma weight residual 1.387 1.468 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C20 U9L E1001 " pdb=" N21 U9L E1001 " ideal model delta sigma weight residual 1.387 1.468 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C20 U9L C 502 " pdb=" N21 U9L C 502 " ideal model delta sigma weight residual 1.387 1.468 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C20 U9L A 502 " pdb=" N21 U9L A 502 " ideal model delta sigma weight residual 1.387 1.465 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C20 U9L D 502 " pdb=" N21 U9L D 502 " ideal model delta sigma weight residual 1.387 1.465 -0.078 2.00e-02 2.50e+03 1.50e+01 ... (remaining 17100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23147 2.39 - 4.77: 192 4.77 - 7.16: 31 7.16 - 9.55: 4 9.55 - 11.94: 1 Bond angle restraints: 23375 Sorted by residual: angle pdb=" CA LEU C 446 " pdb=" CB LEU C 446 " pdb=" CG LEU C 446 " ideal model delta sigma weight residual 116.30 128.24 -11.94 3.50e+00 8.16e-02 1.16e+01 angle pdb=" C ASN B 141 " pdb=" N PHE B 142 " pdb=" CA PHE B 142 " ideal model delta sigma weight residual 121.62 126.57 -4.95 1.57e+00 4.06e-01 9.95e+00 angle pdb=" C ASN D 141 " pdb=" N PHE D 142 " pdb=" CA PHE D 142 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.57e+00 4.06e-01 9.34e+00 angle pdb=" C ASN C 141 " pdb=" N PHE C 142 " pdb=" CA PHE C 142 " ideal model delta sigma weight residual 121.62 126.31 -4.69 1.57e+00 4.06e-01 8.91e+00 angle pdb=" C ASN E 141 " pdb=" N PHE E 142 " pdb=" CA PHE E 142 " ideal model delta sigma weight residual 121.62 126.20 -4.58 1.57e+00 4.06e-01 8.51e+00 ... (remaining 23370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8763 17.99 - 35.98: 842 35.98 - 53.97: 213 53.97 - 71.96: 28 71.96 - 89.95: 14 Dihedral angle restraints: 9860 sinusoidal: 4045 harmonic: 5815 Sorted by residual: dihedral pdb=" CA ASN B 141 " pdb=" C ASN B 141 " pdb=" N PHE B 142 " pdb=" CA PHE B 142 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASN A 141 " pdb=" C ASN A 141 " pdb=" N PHE A 142 " pdb=" CA PHE A 142 " ideal model delta harmonic sigma weight residual -180.00 -163.87 -16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CG ARG D 439 " pdb=" CD ARG D 439 " pdb=" NE ARG D 439 " pdb=" CZ ARG D 439 " ideal model delta sinusoidal sigma weight residual -180.00 -135.75 -44.25 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1880 0.036 - 0.072: 589 0.072 - 0.107: 207 0.107 - 0.143: 79 0.143 - 0.179: 5 Chirality restraints: 2760 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 148 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2757 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 325 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C VAL D 325 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 325 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 326 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 325 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C VAL B 325 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL B 325 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 326 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 325 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C VAL E 325 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL E 325 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 326 " 0.011 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1449 2.75 - 3.28: 16179 3.28 - 3.82: 28648 3.82 - 4.36: 32466 4.36 - 4.90: 58457 Nonbonded interactions: 137199 Sorted by model distance: nonbonded pdb=" OH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 2.248 3.040 ... (remaining 137194 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 460) selection = (chain 'B' and resid 8 through 460) selection = (chain 'C' and resid 8 through 460) selection = (chain 'D' and resid 8 through 460) selection = (chain 'E' and resid 8 through 460) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.330 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17130 Z= 0.184 Angle : 0.607 11.936 23450 Z= 0.310 Chirality : 0.043 0.179 2760 Planarity : 0.004 0.036 2820 Dihedral : 15.214 89.945 6070 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.05 % Allowed : 11.81 % Favored : 88.13 % 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: 1.09 (0.20), residues: 1930 helix: 2.46 (0.18), residues: 815 sheet: -1.62 (0.21), residues: 445 loop : 0.41 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 420 TYR 0.011 0.001 TYR C 67 PHE 0.012 0.001 PHE D 242 TRP 0.018 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (17105) covalent geometry : angle 0.60112 / 0.31 (23375) hydrogen bonds : bond 0.13937 / 9.20 ( 900) hydrogen bonds : angle 6.30575 / 4.45 ( 2736) link_BETA1-4 : bond 0.00313 / 0.16 ( 10) link_BETA1-4 : angle 2.03730 / 1.22 ( 30) link_NAG-ASN : bond 0.00081 / 0.05 ( 15) link_NAG-ASN : angle 1.14877 / 0.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.596 Fit side-chains REVERT: B 410 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6931 (ttp-170) REVERT: E 235 MET cc_start: 0.7769 (tpp) cc_final: 0.7557 (mmm) outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.1388 time to fit residues: 29.1453 Evaluate side-chains 123 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.128936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099762 restraints weight = 19186.878| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.57 r_work: 0.2866 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17130 Z= 0.117 Angle : 0.508 6.258 23450 Z= 0.259 Chirality : 0.042 0.140 2760 Planarity : 0.004 0.032 2820 Dihedral : 4.848 43.995 2227 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.71 % Allowed : 12.58 % Favored : 86.70 % 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: 1.35 (0.20), residues: 1930 helix: 2.59 (0.18), residues: 815 sheet: -1.18 (0.20), residues: 520 loop : 0.66 (0.28), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.017 0.001 TYR A 67 PHE 0.009 0.001 PHE A 242 TRP 0.009 0.001 TRP D 459 HIS 0.003 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17105) covalent geometry : angle 0.50240 / 0.26 (23375) hydrogen bonds : bond 0.04227 / 2.83 ( 900) hydrogen bonds : angle 4.72972 / 3.33 ( 2736) link_BETA1-4 : bond 0.00258 / 0.14 ( 10) link_BETA1-4 : angle 1.57327 / 1.00 ( 30) link_NAG-ASN : bond 0.00094 / 0.05 ( 15) link_NAG-ASN : angle 1.39755 / 0.96 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.536 Fit side-chains REVERT: A 235 MET cc_start: 0.7646 (tpp) cc_final: 0.7312 (mmm) REVERT: B 410 ARG cc_start: 0.7132 (ttp-170) cc_final: 0.6910 (ttp-170) REVERT: C 52 ASP cc_start: 0.8300 (t70) cc_final: 0.7848 (t0) REVERT: C 210 MET cc_start: 0.8684 (tpt) cc_final: 0.8432 (tpt) REVERT: C 235 MET cc_start: 0.7524 (tpp) cc_final: 0.7280 (mmm) REVERT: C 242 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7738 (t80) REVERT: C 415 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7874 (ttpt) REVERT: D 136 SER cc_start: 0.8786 (m) cc_final: 0.8481 (p) REVERT: E 235 MET cc_start: 0.7664 (tpp) cc_final: 0.7382 (mmm) outliers start: 13 outliers final: 6 residues processed: 149 average time/residue: 0.1257 time to fit residues: 28.4285 Evaluate side-chains 136 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 182 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 86 optimal weight: 0.0870 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098916 restraints weight = 19453.682| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.58 r_work: 0.2838 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17130 Z= 0.125 Angle : 0.496 7.145 23450 Z= 0.250 Chirality : 0.042 0.138 2760 Planarity : 0.004 0.031 2820 Dihedral : 4.592 20.333 2225 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.32 % Allowed : 13.52 % Favored : 85.16 % 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: 1.45 (0.20), residues: 1930 helix: 2.85 (0.18), residues: 790 sheet: -1.05 (0.21), residues: 505 loop : 0.40 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.017 0.001 TYR C 67 PHE 0.013 0.001 PHE B 242 TRP 0.012 0.001 TRP D 459 HIS 0.003 0.001 HIS C 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17105) covalent geometry : angle 0.48996 / 0.25 (23375) hydrogen bonds : bond 0.03972 / 2.67 ( 900) hydrogen bonds : angle 4.47686 / 3.15 ( 2736) link_BETA1-4 : bond 0.00289 / 0.16 ( 10) link_BETA1-4 : angle 1.62251 / 1.02 ( 30) link_NAG-ASN : bond 0.00135 / 0.07 ( 15) link_NAG-ASN : angle 1.40758 / 0.96 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.579 Fit side-chains REVERT: A 235 MET cc_start: 0.7629 (tpp) cc_final: 0.7290 (mmm) REVERT: A 311 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7126 (pp30) REVERT: B 311 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7263 (pp30) REVERT: B 410 ARG cc_start: 0.7150 (ttp-170) cc_final: 0.6945 (ttp-170) REVERT: C 52 ASP cc_start: 0.8420 (t70) cc_final: 0.7912 (t0) REVERT: C 54 LYS cc_start: 0.7915 (tptp) cc_final: 0.7487 (tptp) REVERT: C 210 MET cc_start: 0.8662 (tpt) cc_final: 0.8229 (tpt) REVERT: C 242 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7703 (t80) REVERT: C 311 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7061 (pp30) REVERT: C 415 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7896 (ttpt) REVERT: D 136 SER cc_start: 0.8809 (m) cc_final: 0.8520 (p) REVERT: D 311 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7249 (pp30) REVERT: D 427 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8047 (tt) REVERT: E 235 MET cc_start: 0.7601 (tpp) cc_final: 0.7390 (mmm) REVERT: E 311 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7261 (pp30) outliers start: 24 outliers final: 10 residues processed: 149 average time/residue: 0.1397 time to fit residues: 31.2144 Evaluate side-chains 144 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 114 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.125670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.097279 restraints weight = 19506.557| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.65 r_work: 0.2832 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17130 Z= 0.141 Angle : 0.501 6.161 23450 Z= 0.251 Chirality : 0.043 0.141 2760 Planarity : 0.004 0.032 2820 Dihedral : 4.579 19.195 2225 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.48 % Allowed : 14.40 % Favored : 84.12 % 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: 1.39 (0.20), residues: 1930 helix: 2.82 (0.18), residues: 790 sheet: -1.06 (0.21), residues: 505 loop : 0.32 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.017 0.001 TYR A 67 PHE 0.009 0.001 PHE A 254 TRP 0.012 0.001 TRP D 459 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (17105) covalent geometry : angle 0.49411 / 0.25 (23375) hydrogen bonds : bond 0.03887 / 2.60 ( 900) hydrogen bonds : angle 4.38870 / 3.09 ( 2736) link_BETA1-4 : bond 0.00248 / 0.13 ( 10) link_BETA1-4 : angle 1.57397 / 0.99 ( 30) link_NAG-ASN : bond 0.00175 / 0.10 ( 15) link_NAG-ASN : angle 1.48970 / 1.02 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.655 Fit side-chains REVERT: A 235 MET cc_start: 0.7547 (tpp) cc_final: 0.7199 (mmm) REVERT: A 311 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7266 (pp30) REVERT: B 311 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7178 (pp30) REVERT: C 242 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7708 (t80) REVERT: C 311 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7189 (pp30) REVERT: C 415 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7929 (ttpt) REVERT: D 136 SER cc_start: 0.8860 (m) cc_final: 0.8596 (p) REVERT: D 311 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7284 (pp30) REVERT: E 17 ASP cc_start: 0.8152 (m-30) cc_final: 0.7906 (t0) REVERT: E 235 MET cc_start: 0.7612 (tpp) cc_final: 0.7352 (mmm) outliers start: 27 outliers final: 11 residues processed: 149 average time/residue: 0.1406 time to fit residues: 31.5403 Evaluate side-chains 143 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 27 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.124436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.096956 restraints weight = 19693.918| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.53 r_work: 0.2846 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17130 Z= 0.186 Angle : 0.547 7.465 23450 Z= 0.270 Chirality : 0.045 0.208 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.729 20.562 2225 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.59 % Allowed : 14.51 % Favored : 83.90 % 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: 1.23 (0.19), residues: 1930 helix: 2.74 (0.18), residues: 790 sheet: -1.19 (0.21), residues: 480 loop : 0.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 315 TYR 0.018 0.002 TYR C 67 PHE 0.009 0.001 PHE A 254 TRP 0.016 0.001 TRP D 459 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (17105) covalent geometry : angle 0.54020 / 0.27 (23375) hydrogen bonds : bond 0.04031 / 2.70 ( 900) hydrogen bonds : angle 4.41974 / 3.10 ( 2736) link_BETA1-4 : bond 0.00157 / 0.09 ( 10) link_BETA1-4 : angle 1.62761 / 1.02 ( 30) link_NAG-ASN : bond 0.00277 / 0.16 ( 15) link_NAG-ASN : angle 1.66194 / 1.13 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.601 Fit side-chains REVERT: A 136 SER cc_start: 0.8825 (m) cc_final: 0.8593 (p) REVERT: A 235 MET cc_start: 0.7514 (tpp) cc_final: 0.7151 (mmm) REVERT: A 311 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7159 (pp30) REVERT: B 311 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7196 (pp30) REVERT: B 410 ARG cc_start: 0.7099 (ttp-170) cc_final: 0.6890 (ttp-170) REVERT: B 427 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (tt) REVERT: C 242 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7707 (t80) REVERT: C 311 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7171 (pp30) REVERT: C 415 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7890 (ttpt) REVERT: D 136 SER cc_start: 0.8860 (m) cc_final: 0.8653 (p) REVERT: D 311 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7264 (pp30) REVERT: E 235 MET cc_start: 0.7590 (tpp) cc_final: 0.7317 (mmm) REVERT: E 311 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7192 (pp30) outliers start: 29 outliers final: 14 residues processed: 151 average time/residue: 0.1438 time to fit residues: 32.6033 Evaluate side-chains 151 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 54 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.127586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099280 restraints weight = 19167.330| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.60 r_work: 0.2874 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17130 Z= 0.108 Angle : 0.488 6.001 23450 Z= 0.244 Chirality : 0.042 0.150 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.451 16.771 2225 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.59 % Allowed : 15.00 % Favored : 83.41 % 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: 1.44 (0.20), residues: 1930 helix: 2.91 (0.18), residues: 790 sheet: -1.03 (0.21), residues: 505 loop : 0.28 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.016 0.001 TYR A 67 PHE 0.009 0.001 PHE B 242 TRP 0.017 0.001 TRP D 459 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17105) covalent geometry : angle 0.48222 / 0.24 (23375) hydrogen bonds : bond 0.03721 / 2.50 ( 900) hydrogen bonds : angle 4.28558 / 3.01 ( 2736) link_BETA1-4 : bond 0.00287 / 0.15 ( 10) link_BETA1-4 : angle 1.53556 / 0.96 ( 30) link_NAG-ASN : bond 0.00159 / 0.09 ( 15) link_NAG-ASN : angle 1.40698 / 0.96 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.657 Fit side-chains REVERT: A 136 SER cc_start: 0.8793 (m) cc_final: 0.8584 (p) REVERT: A 235 MET cc_start: 0.7623 (tpp) cc_final: 0.7281 (mmm) REVERT: A 311 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7293 (pp30) REVERT: B 311 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7277 (pp30) REVERT: B 427 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7920 (tp) REVERT: C 44 ILE cc_start: 0.8566 (mt) cc_final: 0.8309 (mm) REVERT: C 242 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7701 (t80) REVERT: C 311 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7001 (pp30) REVERT: D 311 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7320 (pp30) REVERT: E 235 MET cc_start: 0.7646 (tpp) cc_final: 0.7376 (mmm) REVERT: E 242 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7104 (t80) REVERT: E 311 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7345 (pp30) REVERT: E 427 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8107 (tp) outliers start: 29 outliers final: 13 residues processed: 163 average time/residue: 0.1421 time to fit residues: 34.9672 Evaluate side-chains 157 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.126835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098184 restraints weight = 19292.843| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.62 r_work: 0.2845 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17130 Z= 0.129 Angle : 0.499 5.849 23450 Z= 0.248 Chirality : 0.043 0.155 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.457 17.528 2225 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.92 % Allowed : 14.89 % 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: 1.42 (0.20), residues: 1930 helix: 2.85 (0.18), residues: 790 sheet: -1.00 (0.21), residues: 505 loop : 0.28 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 315 TYR 0.017 0.001 TYR A 67 PHE 0.009 0.001 PHE A 254 TRP 0.020 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17105) covalent geometry : angle 0.49287 / 0.25 (23375) hydrogen bonds : bond 0.03735 / 2.50 ( 900) hydrogen bonds : angle 4.26405 / 2.99 ( 2736) link_BETA1-4 : bond 0.00228 / 0.13 ( 10) link_BETA1-4 : angle 1.55719 / 0.98 ( 30) link_NAG-ASN : bond 0.00203 / 0.12 ( 15) link_NAG-ASN : angle 1.47738 / 1.02 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.652 Fit side-chains REVERT: A 136 SER cc_start: 0.8815 (m) cc_final: 0.8606 (p) REVERT: A 235 MET cc_start: 0.7648 (tpp) cc_final: 0.7307 (mmm) REVERT: A 311 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7301 (pp30) REVERT: B 311 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7284 (pp30) REVERT: B 427 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7954 (tp) REVERT: C 44 ILE cc_start: 0.8596 (mt) cc_final: 0.8342 (mm) REVERT: C 242 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7705 (t80) REVERT: C 311 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.6991 (pp30) REVERT: D 311 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7324 (pp30) REVERT: E 235 MET cc_start: 0.7652 (tpp) cc_final: 0.7374 (mmm) REVERT: E 311 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7360 (pp30) REVERT: E 427 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8090 (tp) outliers start: 35 outliers final: 19 residues processed: 159 average time/residue: 0.1375 time to fit residues: 33.4256 Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 165 optimal weight: 0.0770 chunk 184 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.125598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.098443 restraints weight = 19354.326| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.55 r_work: 0.2858 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17130 Z= 0.149 Angle : 0.515 6.939 23450 Z= 0.255 Chirality : 0.043 0.163 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.514 18.551 2225 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.76 % Allowed : 15.22 % Favored : 83.02 % 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: 1.32 (0.19), residues: 1930 helix: 2.81 (0.18), residues: 790 sheet: -1.12 (0.22), residues: 480 loop : 0.18 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 315 TYR 0.017 0.001 TYR C 67 PHE 0.010 0.001 PHE B 242 TRP 0.023 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (17105) covalent geometry : angle 0.50825 / 0.25 (23375) hydrogen bonds : bond 0.03791 / 2.53 ( 900) hydrogen bonds : angle 4.28118 / 3.00 ( 2736) link_BETA1-4 : bond 0.00207 / 0.12 ( 10) link_BETA1-4 : angle 1.55737 / 0.98 ( 30) link_NAG-ASN : bond 0.00226 / 0.13 ( 15) link_NAG-ASN : angle 1.53835 / 1.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.558 Fit side-chains REVERT: A 235 MET cc_start: 0.7587 (tpp) cc_final: 0.7242 (mmm) REVERT: A 311 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7223 (pp30) REVERT: B 311 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: B 427 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8032 (tt) REVERT: C 44 ILE cc_start: 0.8632 (mt) cc_final: 0.8370 (mm) REVERT: C 242 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7684 (t80) REVERT: C 311 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7028 (pp30) REVERT: C 406 LEU cc_start: 0.8191 (mt) cc_final: 0.7982 (mt) REVERT: D 52 ASP cc_start: 0.8251 (t70) cc_final: 0.7976 (t70) REVERT: D 311 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7297 (pp30) REVERT: E 235 MET cc_start: 0.7583 (tpp) cc_final: 0.7300 (mmm) REVERT: E 311 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7304 (pp30) REVERT: E 427 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8028 (tp) outliers start: 32 outliers final: 21 residues processed: 152 average time/residue: 0.1345 time to fit residues: 30.9650 Evaluate side-chains 156 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 155 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.127496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.098882 restraints weight = 19284.720| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.63 r_work: 0.2863 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17130 Z= 0.118 Angle : 0.490 6.060 23450 Z= 0.244 Chirality : 0.042 0.162 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.385 16.762 2225 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.70 % Allowed : 15.66 % Favored : 82.64 % 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: 1.48 (0.20), residues: 1930 helix: 2.91 (0.18), residues: 790 sheet: -0.99 (0.21), residues: 505 loop : 0.32 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.016 0.001 TYR C 67 PHE 0.010 0.001 PHE B 242 TRP 0.024 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (17105) covalent geometry : angle 0.48377 / 0.24 (23375) hydrogen bonds : bond 0.03646 / 2.44 ( 900) hydrogen bonds : angle 4.21869 / 2.96 ( 2736) link_BETA1-4 : bond 0.00263 / 0.15 ( 10) link_BETA1-4 : angle 1.53239 / 0.96 ( 30) link_NAG-ASN : bond 0.00157 / 0.09 ( 15) link_NAG-ASN : angle 1.39162 / 0.95 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.657 Fit side-chains REVERT: A 235 MET cc_start: 0.7631 (tpp) cc_final: 0.7296 (mmm) REVERT: A 311 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7311 (pp30) REVERT: B 223 TYR cc_start: 0.7777 (m-80) cc_final: 0.7416 (m-80) REVERT: B 311 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7290 (pp30) REVERT: B 320 TRP cc_start: 0.8506 (p-90) cc_final: 0.8251 (p-90) REVERT: B 427 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 44 ILE cc_start: 0.8581 (mt) cc_final: 0.8334 (mm) REVERT: C 136 SER cc_start: 0.8990 (m) cc_final: 0.8756 (p) REVERT: C 242 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7688 (t80) REVERT: C 311 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7058 (pp30) REVERT: D 197 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7750 (mtpp) REVERT: D 311 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7328 (pp30) REVERT: E 235 MET cc_start: 0.7544 (tpp) cc_final: 0.7282 (mmm) REVERT: E 311 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7389 (pp30) REVERT: E 427 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8106 (tp) outliers start: 31 outliers final: 20 residues processed: 156 average time/residue: 0.1405 time to fit residues: 33.3106 Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS D 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.096058 restraints weight = 19465.296| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.69 r_work: 0.2797 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17130 Z= 0.246 Angle : 0.591 8.271 23450 Z= 0.292 Chirality : 0.046 0.169 2760 Planarity : 0.004 0.038 2820 Dihedral : 4.839 22.174 2225 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.65 % Allowed : 15.60 % Favored : 82.75 % 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: 1.01 (0.19), residues: 1930 helix: 2.57 (0.18), residues: 790 sheet: -1.21 (0.21), residues: 480 loop : -0.09 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.019 0.002 TYR C 67 PHE 0.012 0.002 PHE B 242 TRP 0.025 0.001 TRP D 459 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (17105) covalent geometry : angle 0.58399 / 0.29 (23375) hydrogen bonds : bond 0.04149 / 2.76 ( 900) hydrogen bonds : angle 4.45018 / 3.11 ( 2736) link_BETA1-4 : bond 0.00158 / 0.09 ( 10) link_BETA1-4 : angle 1.62024 / 1.04 ( 30) link_NAG-ASN : bond 0.00369 / 0.22 ( 15) link_NAG-ASN : angle 1.83213 / 1.24 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.575 Fit side-chains REVERT: A 235 MET cc_start: 0.7705 (tpp) cc_final: 0.7347 (mmm) REVERT: A 311 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7204 (pp30) REVERT: B 311 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.7297 (pp30) REVERT: B 427 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8192 (tt) REVERT: C 242 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 311 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7035 (pp30) REVERT: D 311 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7401 (pp30) REVERT: E 235 MET cc_start: 0.7751 (tpp) cc_final: 0.7457 (mmm) REVERT: E 311 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7252 (pp30) REVERT: E 427 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8205 (tp) outliers start: 30 outliers final: 20 residues processed: 155 average time/residue: 0.1373 time to fit residues: 31.6694 Evaluate side-chains 149 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 23 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 94 optimal weight: 0.0670 chunk 172 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 30 optimal weight: 0.0060 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 0.0570 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.1850 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.128171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.099627 restraints weight = 19173.560| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.62 r_work: 0.2873 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 17130 Z= 0.094 Angle : 0.490 6.495 23450 Z= 0.245 Chirality : 0.042 0.154 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.374 16.526 2225 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.59 % Allowed : 16.10 % Favored : 82.31 % 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: 1.45 (0.20), residues: 1930 helix: 2.95 (0.18), residues: 790 sheet: -1.03 (0.21), residues: 505 loop : 0.24 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.015 0.001 TYR C 67 PHE 0.008 0.001 PHE B 242 TRP 0.025 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (17105) covalent geometry : angle 0.48406 / 0.24 (23375) hydrogen bonds : bond 0.03615 / 2.42 ( 900) hydrogen bonds : angle 4.23386 / 2.97 ( 2736) link_BETA1-4 : bond 0.00357 / 0.20 ( 10) link_BETA1-4 : angle 1.50739 / 0.94 ( 30) link_NAG-ASN : bond 0.00152 / 0.09 ( 15) link_NAG-ASN : angle 1.31335 / 0.89 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.00 seconds wall clock time: 67 minutes 14.05 seconds (4034.05 seconds total)