Starting phenix.real_space_refine on Sun Aug 24 03:20:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cc6_16555/08_2025/8cc6_16555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cc6_16555/08_2025/8cc6_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cc6_16555/08_2025/8cc6_16555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cc6_16555/08_2025/8cc6_16555.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cc6_16555/08_2025/8cc6_16555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cc6_16555/08_2025/8cc6_16555.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.17, per 1000 atoms: 0.19 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: 1.18 Conformation dependent library (CDL) restraints added in 488.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.53 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: 2.71 Time building geometry restraints manager: 1.49 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: 9271 17.99 - 35.98: 849 35.98 - 53.97: 223 53.97 - 71.96: 28 71.96 - 89.95: 14 Dihedral angle restraints: 10385 sinusoidal: 4570 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 10382 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.340 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 14.780 89.945 6595 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 aren 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 covalent geometry : bond 0.00375 (17105) covalent geometry : angle 0.60112 (23375) hydrogen bonds : bond 0.13937 ( 900) hydrogen bonds : angle 6.30575 ( 2736) link_BETA1-4 : bond 0.00313 ( 10) link_BETA1-4 : angle 2.03730 ( 30) link_NAG-ASN : bond 0.00081 ( 15) link_NAG-ASN : angle 1.14877 ( 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 : 0.551 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: 0.1184 time to fit residues: 24.8940 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 : 0.363 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.129098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099479 restraints weight = 19179.325| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.61 r_work: 0.2870 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 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 = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17130 Z= 0.117 Angle : 0.508 6.161 23450 Z= 0.258 Chirality : 0.043 0.142 2760 Planarity : 0.004 0.032 2820 Dihedral : 5.314 44.269 2752 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 aren 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 0.003 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 covalent geometry : bond 0.00257 (17105) covalent geometry : angle 0.50140 (23375) hydrogen bonds : bond 0.04161 ( 900) hydrogen bonds : angle 4.70151 ( 2736) link_BETA1-4 : bond 0.00353 ( 10) link_BETA1-4 : angle 1.68283 ( 30) link_NAG-ASN : bond 0.00107 ( 15) link_NAG-ASN : angle 1.34766 ( 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 154 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.633 Fit side-chains REVERT: A 235 MET cc_start: 0.7641 (tpp) cc_final: 0.7335 (mmm) REVERT: B 410 ARG cc_start: 0.7125 (ttp-170) cc_final: 0.6900 (ttp-170) REVERT: C 52 ASP cc_start: 0.8294 (t70) cc_final: 0.7841 (t0) REVERT: C 235 MET cc_start: 0.7483 (tpp) cc_final: 0.7191 (mmm) REVERT: C 242 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7723 (t80) REVERT: C 415 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7863 (ttpt) REVERT: D 136 SER cc_start: 0.8790 (m) cc_final: 0.8484 (p) REVERT: D 197 LYS cc_start: 0.7988 (mttm) cc_final: 0.7784 (mtpp) REVERT: E 235 MET cc_start: 0.7652 (tpp) cc_final: 0.7359 (mmm) outliers start: 13 outliers final: 6 residues processed: 148 average time/residue: 0.1227 time to fit residues: 27.1817 Evaluate side-chains 137 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 86 optimal weight: 0.0980 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.100103 restraints weight = 19414.359| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.58 r_work: 0.2857 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- 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: 5 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17130 Z= 0.108 Angle : 0.481 7.453 23450 Z= 0.243 Chirality : 0.042 0.137 2760 Planarity : 0.004 0.030 2820 Dihedral : 4.693 33.637 2750 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.37 % Allowed : 13.57 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.20), residues: 1930 helix: 2.90 (0.18), residues: 790 sheet: -1.13 (0.21), residues: 515 loop : 0.52 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 315 TYR 0.017 0.001 TYR C 67 PHE 0.010 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 covalent geometry : bond 0.00238 (17105) covalent geometry : angle 0.47441 (23375) hydrogen bonds : bond 0.03876 ( 900) hydrogen bonds : angle 4.43663 ( 2736) link_BETA1-4 : bond 0.00287 ( 10) link_BETA1-4 : angle 1.82661 ( 30) link_NAG-ASN : bond 0.00124 ( 15) link_NAG-ASN : angle 1.27241 ( 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 156 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.579 Fit side-chains REVERT: A 235 MET cc_start: 0.7630 (tpp) cc_final: 0.7288 (mmm) REVERT: A 311 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7136 (pp30) REVERT: B 311 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: C 50 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8483 (t0) REVERT: C 52 ASP cc_start: 0.8364 (t70) cc_final: 0.7867 (t0) REVERT: C 242 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7666 (t80) REVERT: C 311 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7150 (pp30) REVERT: C 415 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7904 (ttpt) REVERT: D 136 SER cc_start: 0.8812 (m) cc_final: 0.8511 (p) REVERT: D 311 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7256 (pp30) REVERT: D 427 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7961 (tp) REVERT: E 235 MET cc_start: 0.7589 (tpp) cc_final: 0.7382 (mmm) REVERT: E 311 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7207 (pp30) outliers start: 25 outliers final: 9 residues processed: 148 average time/residue: 0.1355 time to fit residues: 29.6626 Evaluate side-chains 141 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 50 ASN 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 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 114 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.124138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.095759 restraints weight = 19622.916| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.73 r_work: 0.2784 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17130 Z= 0.214 Angle : 0.562 6.935 23450 Z= 0.280 Chirality : 0.045 0.150 2760 Planarity : 0.004 0.035 2820 Dihedral : 4.997 32.054 2750 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.54 % Allowed : 14.40 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.19), residues: 1930 helix: 2.68 (0.18), residues: 790 sheet: -1.20 (0.21), residues: 480 loop : 0.12 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.018 0.002 TYR C 67 PHE 0.021 0.002 PHE B 242 TRP 0.015 0.001 TRP D 459 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00528 (17105) covalent geometry : angle 0.55450 (23375) hydrogen bonds : bond 0.04181 ( 900) hydrogen bonds : angle 4.50557 ( 2736) link_BETA1-4 : bond 0.00137 ( 10) link_BETA1-4 : angle 1.86829 ( 30) link_NAG-ASN : bond 0.00342 ( 15) link_NAG-ASN : angle 1.62556 ( 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 164 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.562 Fit side-chains REVERT: A 136 SER cc_start: 0.8826 (m) cc_final: 0.8597 (p) REVERT: A 235 MET cc_start: 0.7554 (tpp) cc_final: 0.7208 (mmm) REVERT: A 311 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7218 (pp30) REVERT: B 311 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7192 (pp30) REVERT: B 410 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6910 (ttp-170) REVERT: C 44 ILE cc_start: 0.8664 (mt) cc_final: 0.8386 (mm) REVERT: C 242 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7731 (t80) REVERT: C 311 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7125 (pp30) REVERT: C 415 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7948 (ttpt) REVERT: D 136 SER cc_start: 0.8876 (m) cc_final: 0.8622 (p) REVERT: D 172 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: D 311 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7298 (pp30) REVERT: D 427 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8153 (tt) REVERT: E 17 ASP cc_start: 0.8161 (m-30) cc_final: 0.7945 (t0) REVERT: E 235 MET cc_start: 0.7691 (tpp) cc_final: 0.7408 (mmm) REVERT: E 311 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7129 (pp30) outliers start: 28 outliers final: 10 residues processed: 157 average time/residue: 0.1211 time to fit residues: 28.7529 Evaluate side-chains 145 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 311 GLN Chi-restraints excluded: chain C residue 146 VAL 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 C residue 332 ILE Chi-restraints excluded: chain D residue 172 GLU 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 311 GLN 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: 0.9990 chunk 167 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 177 optimal weight: 0.0050 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 166 optimal weight: 0.0470 chunk 112 optimal weight: 3.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101041 restraints weight = 19312.473| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.71 r_work: 0.2849 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17130 Z= 0.099 Angle : 0.484 7.000 23450 Z= 0.242 Chirality : 0.042 0.202 2760 Planarity : 0.004 0.032 2820 Dihedral : 4.466 23.151 2750 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.59 % Allowed : 14.45 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.20), residues: 1930 helix: 2.92 (0.18), residues: 790 sheet: -1.04 (0.21), residues: 505 loop : 0.33 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 315 TYR 0.016 0.001 TYR C 67 PHE 0.007 0.001 PHE C 233 TRP 0.017 0.001 TRP D 459 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00211 (17105) covalent geometry : angle 0.47744 (23375) hydrogen bonds : bond 0.03698 ( 900) hydrogen bonds : angle 4.29618 ( 2736) link_BETA1-4 : bond 0.00337 ( 10) link_BETA1-4 : angle 1.80171 ( 30) link_NAG-ASN : bond 0.00116 ( 15) link_NAG-ASN : angle 1.27697 ( 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 167 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.647 Fit side-chains REVERT: A 235 MET cc_start: 0.7624 (tpp) cc_final: 0.7291 (mmm) REVERT: A 311 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7255 (pp30) REVERT: A 427 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8098 (tp) REVERT: B 311 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7264 (pp30) REVERT: B 427 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7963 (tp) REVERT: C 44 ILE cc_start: 0.8560 (mt) cc_final: 0.8330 (mm) REVERT: C 242 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7697 (t80) REVERT: C 311 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.6946 (pp30) REVERT: C 415 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7942 (ttpt) REVERT: D 52 ASP cc_start: 0.8221 (t70) cc_final: 0.7954 (t70) REVERT: D 136 SER cc_start: 0.8807 (m) cc_final: 0.8581 (p) REVERT: D 311 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7404 (pp30) REVERT: D 427 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8146 (tt) REVERT: E 235 MET cc_start: 0.7620 (tpp) cc_final: 0.7368 (mmm) REVERT: E 311 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7307 (pp30) outliers start: 29 outliers final: 11 residues processed: 161 average time/residue: 0.1287 time to fit residues: 30.7055 Evaluate side-chains 156 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU 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 311 GLN 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 410 ARG Chi-restraints excluded: chain D residue 427 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: 1.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 87 optimal weight: 0.0050 chunk 119 optimal weight: 0.0470 chunk 20 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 overall best weight: 1.0096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 460 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.126625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097386 restraints weight = 19246.875| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.82 r_work: 0.2816 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1213 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= 0.140 Angle : 0.505 5.890 23450 Z= 0.251 Chirality : 0.043 0.158 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.469 18.717 2750 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.87 % Allowed : 14.45 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.19), residues: 1930 helix: 2.81 (0.18), residues: 790 sheet: -1.03 (0.21), residues: 505 loop : 0.26 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 315 TYR 0.017 0.001 TYR C 67 PHE 0.009 0.001 PHE B 242 TRP 0.018 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00329 (17105) covalent geometry : angle 0.49771 (23375) hydrogen bonds : bond 0.03783 ( 900) hydrogen bonds : angle 4.29924 ( 2736) link_BETA1-4 : bond 0.00185 ( 10) link_BETA1-4 : angle 1.81439 ( 30) link_NAG-ASN : bond 0.00226 ( 15) link_NAG-ASN : angle 1.41464 ( 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 174 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.620 Fit side-chains REVERT: A 136 SER cc_start: 0.8889 (m) cc_final: 0.8657 (p) REVERT: A 235 MET cc_start: 0.7596 (tpp) cc_final: 0.7252 (mmm) REVERT: A 311 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7207 (pp30) REVERT: B 311 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7242 (pp30) REVERT: B 427 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7924 (tp) REVERT: C 44 ILE cc_start: 0.8627 (mt) cc_final: 0.8368 (mm) REVERT: C 242 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7703 (t80) REVERT: C 311 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7005 (pp30) REVERT: C 415 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7858 (ttpt) REVERT: D 52 ASP cc_start: 0.8223 (t70) cc_final: 0.7941 (t70) REVERT: D 311 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7334 (pp30) REVERT: D 427 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8107 (tt) REVERT: E 235 MET cc_start: 0.7560 (tpp) cc_final: 0.7300 (mmm) REVERT: E 242 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.6971 (t80) REVERT: E 311 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7246 (pp30) REVERT: E 427 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8073 (tp) outliers start: 34 outliers final: 17 residues processed: 165 average time/residue: 0.1356 time to fit residues: 33.1646 Evaluate side-chains 163 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 B residue 427 LEU Chi-restraints excluded: chain C residue 76 THR 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 446 LEU 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 410 ARG Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 76 THR 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: 2.9990 chunk 51 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.126468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.097587 restraints weight = 19321.038| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.67 r_work: 0.2823 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1268 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= 0.141 Angle : 0.505 5.893 23450 Z= 0.251 Chirality : 0.043 0.147 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.450 18.264 2750 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.98 % Allowed : 14.89 % Favored : 83.13 % 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 aren not related in a simple way. whole: 1.35 (0.19), residues: 1930 helix: 2.83 (0.18), residues: 790 sheet: -1.12 (0.21), residues: 480 loop : 0.21 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 315 TYR 0.017 0.001 TYR C 67 PHE 0.009 0.001 PHE B 242 TRP 0.020 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00334 (17105) covalent geometry : angle 0.49799 (23375) hydrogen bonds : bond 0.03775 ( 900) hydrogen bonds : angle 4.28390 ( 2736) link_BETA1-4 : bond 0.00241 ( 10) link_BETA1-4 : angle 1.81150 ( 30) link_NAG-ASN : bond 0.00209 ( 15) link_NAG-ASN : angle 1.41136 ( 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 172 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.388 Fit side-chains REVERT: A 136 SER cc_start: 0.8879 (m) cc_final: 0.8679 (p) REVERT: A 235 MET cc_start: 0.7648 (tpp) cc_final: 0.7307 (mmm) REVERT: A 311 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7241 (pp30) REVERT: B 223 TYR cc_start: 0.7799 (m-80) cc_final: 0.7446 (m-80) REVERT: B 311 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7291 (pp30) REVERT: B 427 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8129 (tt) REVERT: C 44 ILE cc_start: 0.8635 (mt) cc_final: 0.8391 (mm) REVERT: C 242 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7727 (t80) REVERT: C 311 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7065 (pp30) REVERT: D 52 ASP cc_start: 0.8277 (t70) cc_final: 0.8010 (t70) REVERT: D 311 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7362 (pp30) REVERT: D 427 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8155 (tt) REVERT: E 235 MET cc_start: 0.7630 (tpp) cc_final: 0.7363 (mmm) REVERT: E 242 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7001 (t80) REVERT: E 311 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7382 (pp30) REVERT: E 427 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8116 (tp) outliers start: 36 outliers final: 20 residues processed: 161 average time/residue: 0.1220 time to fit residues: 29.5765 Evaluate side-chains 165 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 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 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 311 GLN Chi-restraints excluded: chain D residue 410 ARG 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 242 PHE 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: 0.7980 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.128925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.100543 restraints weight = 19229.110| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.70 r_work: 0.2828 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1320 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= 0.124 Angle : 0.493 6.241 23450 Z= 0.245 Chirality : 0.043 0.161 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.345 17.340 2750 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.87 % Allowed : 14.89 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.20), residues: 1930 helix: 2.88 (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 0.016 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 covalent geometry : bond 0.00286 (17105) covalent geometry : angle 0.48547 (23375) hydrogen bonds : bond 0.03678 ( 900) hydrogen bonds : angle 4.24026 ( 2736) link_BETA1-4 : bond 0.00270 ( 10) link_BETA1-4 : angle 1.81339 ( 30) link_NAG-ASN : bond 0.00169 ( 15) link_NAG-ASN : angle 1.35194 ( 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 178 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.667 Fit side-chains REVERT: A 235 MET cc_start: 0.7613 (tpp) cc_final: 0.7279 (mmm) REVERT: A 311 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7228 (pp30) REVERT: B 223 TYR cc_start: 0.7750 (m-80) cc_final: 0.7325 (m-80) REVERT: B 311 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7342 (pp30) REVERT: B 427 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7988 (tp) REVERT: C 44 ILE cc_start: 0.8614 (mt) cc_final: 0.8371 (mm) REVERT: C 136 SER cc_start: 0.8992 (m) cc_final: 0.8760 (p) REVERT: C 242 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7683 (t80) REVERT: C 311 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7023 (pp30) REVERT: D 197 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7753 (mtpp) REVERT: D 311 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7329 (pp30) REVERT: D 427 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8120 (tt) REVERT: E 235 MET cc_start: 0.7488 (tpp) cc_final: 0.7223 (mmm) REVERT: E 311 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7415 (pp30) REVERT: E 427 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8076 (tp) outliers start: 34 outliers final: 20 residues processed: 169 average time/residue: 0.1312 time to fit residues: 33.4782 Evaluate side-chains 168 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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 410 ARG Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain E residue 76 THR 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: 0.8980 chunk 90 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 155 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.100920 restraints weight = 19240.091| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.73 r_work: 0.2857 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17130 Z= 0.102 Angle : 0.477 5.746 23450 Z= 0.239 Chirality : 0.042 0.158 2760 Planarity : 0.004 0.031 2820 Dihedral : 4.206 15.944 2750 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.59 % Allowed : 15.66 % 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 aren not related in a simple way. whole: 1.55 (0.20), residues: 1930 helix: 2.94 (0.18), residues: 790 sheet: -0.96 (0.21), residues: 505 loop : 0.42 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 315 TYR 0.016 0.001 TYR C 67 PHE 0.012 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 covalent geometry : bond 0.00222 (17105) covalent geometry : angle 0.47011 (23375) hydrogen bonds : bond 0.03549 ( 900) hydrogen bonds : angle 4.17769 ( 2736) link_BETA1-4 : bond 0.00314 ( 10) link_BETA1-4 : angle 1.78501 ( 30) link_NAG-ASN : bond 0.00130 ( 15) link_NAG-ASN : angle 1.23959 ( 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 168 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.654 Fit side-chains REVERT: A 235 MET cc_start: 0.7658 (tpp) cc_final: 0.7336 (mmm) REVERT: A 311 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7321 (pp30) REVERT: B 223 TYR cc_start: 0.7682 (m-80) cc_final: 0.7193 (m-80) REVERT: B 311 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.7317 (pp30) REVERT: B 320 TRP cc_start: 0.8476 (p-90) cc_final: 0.8235 (p-90) REVERT: B 427 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7887 (tp) REVERT: C 20 LEU cc_start: 0.8505 (mt) cc_final: 0.8194 (mp) REVERT: C 44 ILE cc_start: 0.8558 (mt) cc_final: 0.8326 (mm) REVERT: C 54 LYS cc_start: 0.7917 (tptp) cc_final: 0.7588 (tptt) REVERT: C 136 SER cc_start: 0.8949 (m) cc_final: 0.8711 (p) REVERT: C 202 ASP cc_start: 0.8231 (t0) cc_final: 0.8030 (t70) REVERT: C 242 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 311 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7042 (pp30) REVERT: D 197 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7807 (mtpp) REVERT: D 311 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7358 (pp30) REVERT: D 427 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8167 (tt) REVERT: E 103 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: E 235 MET cc_start: 0.7522 (tpp) cc_final: 0.7272 (mmm) REVERT: E 311 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: E 427 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8147 (tp) outliers start: 29 outliers final: 16 residues processed: 161 average time/residue: 0.1340 time to fit residues: 32.1340 Evaluate side-chains 161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 250 GLU 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 201 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 242 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 410 ARG Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 103 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=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: 0.5980 chunk 160 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 0.0670 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 0.0980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100570 restraints weight = 19231.944| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.52 r_work: 0.2878 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17130 Z= 0.133 Angle : 0.493 5.774 23450 Z= 0.246 Chirality : 0.043 0.158 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.294 17.915 2750 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.70 % Allowed : 15.49 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.20), residues: 1930 helix: 2.86 (0.18), residues: 790 sheet: -0.96 (0.21), residues: 505 loop : 0.33 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 315 TYR 0.016 0.001 TYR C 67 PHE 0.008 0.001 PHE A 254 TRP 0.025 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00311 (17105) covalent geometry : angle 0.48640 (23375) hydrogen bonds : bond 0.03648 ( 900) hydrogen bonds : angle 4.20801 ( 2736) link_BETA1-4 : bond 0.00255 ( 10) link_BETA1-4 : angle 1.80797 ( 30) link_NAG-ASN : bond 0.00178 ( 15) link_NAG-ASN : angle 1.35445 ( 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 169 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.678 Fit side-chains REVERT: A 235 MET cc_start: 0.7642 (tpp) cc_final: 0.7317 (mmm) REVERT: A 311 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7328 (pp30) REVERT: B 223 TYR cc_start: 0.7760 (m-80) cc_final: 0.7340 (m-80) REVERT: B 311 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7310 (pp30) REVERT: B 320 TRP cc_start: 0.8478 (p-90) cc_final: 0.8227 (p-90) REVERT: B 427 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8004 (tp) REVERT: C 44 ILE cc_start: 0.8597 (mt) cc_final: 0.8359 (mm) REVERT: C 54 LYS cc_start: 0.7965 (tptp) cc_final: 0.7665 (tptt) REVERT: C 136 SER cc_start: 0.8950 (m) cc_final: 0.8729 (p) REVERT: C 242 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7749 (t80) REVERT: C 311 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7062 (pp30) REVERT: D 197 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7733 (mtpp) REVERT: D 311 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7351 (pp30) REVERT: D 427 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8132 (tt) REVERT: E 103 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8011 (m-10) REVERT: E 235 MET cc_start: 0.7500 (tpp) cc_final: 0.7242 (mmm) REVERT: E 311 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: E 427 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8135 (tp) outliers start: 31 outliers final: 18 residues processed: 160 average time/residue: 0.1348 time to fit residues: 32.3887 Evaluate side-chains 165 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 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 242 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 410 ARG Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 103 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 23 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 172 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.100020 restraints weight = 19297.916| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.67 r_work: 0.2870 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1442 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= 0.119 Angle : 0.486 6.179 23450 Z= 0.242 Chirality : 0.042 0.157 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.264 17.275 2750 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 15.44 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.20), residues: 1930 helix: 2.88 (0.18), residues: 790 sheet: -0.94 (0.21), residues: 505 loop : 0.37 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 315 TYR 0.016 0.001 TYR C 67 PHE 0.010 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 covalent geometry : bond 0.00271 (17105) covalent geometry : angle 0.47870 (23375) hydrogen bonds : bond 0.03595 ( 900) hydrogen bonds : angle 4.20001 ( 2736) link_BETA1-4 : bond 0.00283 ( 10) link_BETA1-4 : angle 1.78762 ( 30) link_NAG-ASN : bond 0.00144 ( 15) link_NAG-ASN : angle 1.30659 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.80 seconds wall clock time: 61 minutes 8.15 seconds (3668.15 seconds total)