Starting phenix.real_space_refine on Sun May 18 06:17:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cc6_16555/05_2025/8cc6_16555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cc6_16555/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cc6_16555/05_2025/8cc6_16555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cc6_16555/05_2025/8cc6_16555.map" model { file = "/net/cci-nas-00/data/ceres_data/8cc6_16555/05_2025/8cc6_16555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cc6_16555/05_2025/8cc6_16555.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.76, per 1000 atoms: 0.59 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: 4.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.72 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: 5.65 Time building geometry restraints manager: 4.76 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 460) selection = (chain 'B' and resid 8 through 460) selection = (chain 'C' and resid 8 through 460) selection = (chain 'D' and resid 8 through 460) selection = (chain 'E' and resid 8 through 460) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.180 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (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 TRP 0.018 0.001 TRP D 459 HIS 0.004 0.001 HIS C 323 PHE 0.012 0.001 PHE D 242 TYR 0.011 0.001 TYR C 67 ARG 0.009 0.000 ARG E 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 15) link_NAG-ASN : angle 1.14877 ( 45) link_BETA1-4 : bond 0.00313 ( 10) link_BETA1-4 : angle 2.03730 ( 30) hydrogen bonds : bond 0.13937 ( 900) hydrogen bonds : angle 6.30575 ( 2736) covalent geometry : bond 0.00375 (17105) covalent geometry : angle 0.60112 (23375) *********************** 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 : 1.657 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: 0.3062 time to fit residues: 63.8544 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 : 2.385 ------------------------------------------------------------------------------- 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 164 optimal weight: 0.0170 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.127735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.098544 restraints weight = 19373.937| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.56 r_work: 0.2835 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17130 Z= 0.159 Angle : 0.536 6.401 23450 Z= 0.271 Chirality : 0.044 0.141 2760 Planarity : 0.004 0.033 2820 Dihedral : 5.532 47.323 2752 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.71 % Allowed : 13.19 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1930 helix: 2.49 (0.18), residues: 815 sheet: -1.28 (0.21), residues: 495 loop : 0.50 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 156 HIS 0.003 0.001 HIS E 323 PHE 0.009 0.001 PHE A 242 TYR 0.018 0.002 TYR A 67 ARG 0.004 0.000 ARG D 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 1.48975 ( 45) link_BETA1-4 : bond 0.00210 ( 10) link_BETA1-4 : angle 1.76415 ( 30) hydrogen bonds : bond 0.04367 ( 900) hydrogen bonds : angle 4.75604 ( 2736) covalent geometry : bond 0.00378 (17105) covalent geometry : angle 0.52956 (23375) *********************** 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 150 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 1.946 Fit side-chains REVERT: A 235 MET cc_start: 0.7702 (tpp) cc_final: 0.7359 (mmm) REVERT: A 242 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8347 (t80) REVERT: B 417 ASP cc_start: 0.8035 (t0) cc_final: 0.7816 (t0) REVERT: C 50 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8364 (t0) REVERT: C 210 MET cc_start: 0.8697 (tpt) cc_final: 0.8424 (tpt) REVERT: C 235 MET cc_start: 0.7560 (tpp) cc_final: 0.7297 (mmm) REVERT: C 242 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 415 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7929 (ttpt) REVERT: D 136 SER cc_start: 0.8800 (m) cc_final: 0.8500 (p) REVERT: E 235 MET cc_start: 0.7717 (tpp) cc_final: 0.7402 (mmm) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 0.3067 time to fit residues: 66.4427 Evaluate side-chains 136 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU 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 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 8 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.122520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.092947 restraints weight = 19607.754| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.64 r_work: 0.2772 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 17130 Z= 0.231 Angle : 0.584 7.322 23450 Z= 0.293 Chirality : 0.046 0.151 2760 Planarity : 0.004 0.036 2820 Dihedral : 5.597 49.007 2750 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.70 % Allowed : 14.45 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1930 helix: 2.32 (0.18), residues: 815 sheet: -1.30 (0.21), residues: 480 loop : 0.08 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 156 HIS 0.003 0.001 HIS C 323 PHE 0.011 0.002 PHE B 242 TYR 0.019 0.002 TYR C 67 ARG 0.003 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 15) link_NAG-ASN : angle 1.74850 ( 45) link_BETA1-4 : bond 0.00130 ( 10) link_BETA1-4 : angle 1.92801 ( 30) hydrogen bonds : bond 0.04478 ( 900) hydrogen bonds : angle 4.67059 ( 2736) covalent geometry : bond 0.00569 (17105) covalent geometry : angle 0.57573 (23375) *********************** 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 161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.898 Fit side-chains REVERT: A 136 SER cc_start: 0.8821 (m) cc_final: 0.8598 (p) REVERT: A 311 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7013 (pp30) REVERT: B 311 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7126 (pp30) REVERT: C 50 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8394 (t0) REVERT: C 242 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7668 (t80) REVERT: C 311 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7041 (pp30) REVERT: C 415 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7850 (ttpt) REVERT: D 136 SER cc_start: 0.8866 (m) cc_final: 0.8617 (p) REVERT: D 172 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: D 311 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7199 (pp30) REVERT: E 17 ASP cc_start: 0.8130 (m-30) cc_final: 0.7823 (t0) REVERT: E 235 MET cc_start: 0.7626 (tpp) cc_final: 0.7377 (mmm) REVERT: E 311 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.6818 (pp30) REVERT: E 417 ASP cc_start: 0.8089 (t0) cc_final: 0.7862 (t0) outliers start: 31 outliers final: 12 residues processed: 153 average time/residue: 0.3092 time to fit residues: 70.7307 Evaluate side-chains 138 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain 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 C residue 332 ILE Chi-restraints excluded: chain C residue 445 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 45 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.124985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095818 restraints weight = 19475.571| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.61 r_work: 0.2830 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 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 = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17130 Z= 0.132 Angle : 0.507 6.388 23450 Z= 0.254 Chirality : 0.043 0.144 2760 Planarity : 0.004 0.034 2820 Dihedral : 5.107 43.653 2750 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.76 % Allowed : 15.22 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 1930 helix: 2.74 (0.18), residues: 790 sheet: -1.17 (0.21), residues: 505 loop : 0.10 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 459 HIS 0.003 0.001 HIS D 323 PHE 0.010 0.001 PHE B 242 TYR 0.017 0.001 TYR D 64 ARG 0.005 0.000 ARG D 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 15) link_NAG-ASN : angle 1.43349 ( 45) link_BETA1-4 : bond 0.00323 ( 10) link_BETA1-4 : angle 1.82446 ( 30) hydrogen bonds : bond 0.03958 ( 900) hydrogen bonds : angle 4.46178 ( 2736) covalent geometry : bond 0.00304 (17105) covalent geometry : angle 0.50006 (23375) *********************** 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 169 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.686 Fit side-chains REVERT: A 136 SER cc_start: 0.8836 (m) cc_final: 0.8601 (p) REVERT: A 235 MET cc_start: 0.7427 (tpp) cc_final: 0.7058 (mmm) REVERT: A 311 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7037 (pp30) REVERT: B 311 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7143 (pp30) REVERT: B 427 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8024 (tt) REVERT: C 44 ILE cc_start: 0.8580 (mt) cc_final: 0.8278 (mm) REVERT: C 242 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7611 (t80) REVERT: C 311 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7051 (pp30) REVERT: C 415 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7825 (ttpt) REVERT: C 427 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7900 (tp) REVERT: D 136 SER cc_start: 0.8860 (m) cc_final: 0.8619 (p) REVERT: D 311 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7205 (pp30) REVERT: E 17 ASP cc_start: 0.8059 (m-30) cc_final: 0.7799 (t0) REVERT: E 235 MET cc_start: 0.7511 (tpp) cc_final: 0.7239 (mmm) REVERT: E 417 ASP cc_start: 0.8067 (t0) cc_final: 0.7812 (t0) REVERT: E 427 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7958 (tp) outliers start: 32 outliers final: 14 residues processed: 159 average time/residue: 0.2875 time to fit residues: 68.6432 Evaluate side-chains 157 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 410 ARG Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 427 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 446 LEU Chi-restraints excluded: chain E residue 86 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 111 optimal weight: 1.9990 chunk 158 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 164 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 136 optimal weight: 0.0570 chunk 60 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 overall best weight: 0.3236 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.130266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101312 restraints weight = 19353.273| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.56 r_work: 0.2904 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17130 Z= 0.093 Angle : 0.477 7.724 23450 Z= 0.239 Chirality : 0.042 0.237 2760 Planarity : 0.004 0.031 2820 Dihedral : 4.465 30.510 2750 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.70 % Allowed : 14.84 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1930 helix: 2.96 (0.18), residues: 790 sheet: -0.99 (0.21), residues: 500 loop : 0.24 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 459 HIS 0.003 0.000 HIS D 323 PHE 0.010 0.001 PHE A 242 TYR 0.016 0.001 TYR A 67 ARG 0.005 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 15) link_NAG-ASN : angle 1.22388 ( 45) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.82640 ( 30) hydrogen bonds : bond 0.03637 ( 900) hydrogen bonds : angle 4.28023 ( 2736) covalent geometry : bond 0.00190 (17105) covalent geometry : angle 0.47057 (23375) *********************** 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: 31 poor density : 136 time to evaluate : 1.902 Fit side-chains REVERT: A 136 SER cc_start: 0.8831 (m) cc_final: 0.8576 (p) REVERT: A 235 MET cc_start: 0.7472 (tpp) cc_final: 0.7109 (mmm) REVERT: A 311 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7094 (pp30) REVERT: A 427 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7921 (tp) REVERT: B 311 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7224 (pp30) REVERT: B 427 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7712 (tp) REVERT: C 44 ILE cc_start: 0.8482 (mt) cc_final: 0.8228 (mm) REVERT: C 50 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8516 (t0) REVERT: C 242 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7569 (t80) REVERT: C 311 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.6910 (pp30) REVERT: C 427 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7881 (tp) REVERT: D 136 SER cc_start: 0.8802 (m) cc_final: 0.8596 (p) REVERT: D 197 LYS cc_start: 0.7891 (mttm) cc_final: 0.7671 (mtpp) REVERT: D 311 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7310 (pp30) REVERT: E 17 ASP cc_start: 0.8094 (m-30) cc_final: 0.7839 (t0) REVERT: E 235 MET cc_start: 0.7426 (tpp) cc_final: 0.7156 (mmm) REVERT: E 311 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7258 (pp30) REVERT: E 417 ASP cc_start: 0.8037 (t0) cc_final: 0.7773 (t0) outliers start: 31 outliers final: 13 residues processed: 160 average time/residue: 0.2930 time to fit residues: 70.6281 Evaluate side-chains 156 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 250 GLU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 50 ASN 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 427 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 410 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 323 HIS D 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094047 restraints weight = 19827.748| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.66 r_work: 0.2798 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- 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: 6 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17130 Z= 0.251 Angle : 0.587 7.869 23450 Z= 0.290 Chirality : 0.046 0.151 2760 Planarity : 0.004 0.037 2820 Dihedral : 4.977 31.349 2750 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.42 % Allowed : 14.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 1930 helix: 2.59 (0.18), residues: 790 sheet: -1.21 (0.21), residues: 480 loop : -0.13 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 459 HIS 0.004 0.001 HIS D 323 PHE 0.012 0.002 PHE A 254 TYR 0.019 0.002 TYR C 67 ARG 0.005 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 15) link_NAG-ASN : angle 1.73721 ( 45) link_BETA1-4 : bond 0.00181 ( 10) link_BETA1-4 : angle 1.89201 ( 30) hydrogen bonds : bond 0.04205 ( 900) hydrogen bonds : angle 4.47992 ( 2736) covalent geometry : bond 0.00619 (17105) covalent geometry : angle 0.57907 (23375) *********************** 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 181 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 1.665 Fit side-chains REVERT: A 235 MET cc_start: 0.7584 (tpp) cc_final: 0.7303 (mmm) REVERT: A 311 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7234 (pp30) REVERT: A 454 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7577 (p) REVERT: B 52 ASP cc_start: 0.8506 (t70) cc_final: 0.8246 (t0) REVERT: B 311 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7240 (pp30) REVERT: B 427 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8118 (tt) REVERT: C 242 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7794 (t80) REVERT: C 311 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7124 (pp30) REVERT: D 311 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7333 (pp30) REVERT: D 454 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7324 (p) REVERT: E 235 MET cc_start: 0.7679 (tpp) cc_final: 0.7386 (mmm) REVERT: E 311 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7277 (pp30) REVERT: E 417 ASP cc_start: 0.8191 (t0) cc_final: 0.7955 (t0) outliers start: 44 outliers final: 24 residues processed: 174 average time/residue: 0.2841 time to fit residues: 74.1845 Evaluate side-chains 160 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 454 THR 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 410 ARG Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 268 ILE 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 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 33 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 109 optimal weight: 0.2980 chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.127079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100219 restraints weight = 19274.123| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.48 r_work: 0.2865 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1291 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 : 0.501 6.200 23450 Z= 0.250 Chirality : 0.043 0.144 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.592 24.765 2750 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.87 % Allowed : 15.77 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1930 helix: 2.83 (0.18), residues: 790 sheet: -1.10 (0.21), residues: 505 loop : 0.05 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 459 HIS 0.003 0.001 HIS B 323 PHE 0.011 0.001 PHE B 242 TYR 0.017 0.001 TYR D 64 ARG 0.006 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 15) link_NAG-ASN : angle 1.40316 ( 45) link_BETA1-4 : bond 0.00291 ( 10) link_BETA1-4 : angle 1.83538 ( 30) hydrogen bonds : bond 0.03792 ( 900) hydrogen bonds : angle 4.33098 ( 2736) covalent geometry : bond 0.00269 (17105) covalent geometry : angle 0.49327 (23375) *********************** 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 168 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.838 Fit side-chains REVERT: A 58 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8433 (tp) REVERT: A 235 MET cc_start: 0.7602 (tpp) cc_final: 0.7223 (mmm) REVERT: A 311 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7173 (pp30) REVERT: B 311 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: B 427 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7936 (tp) REVERT: C 44 ILE cc_start: 0.8611 (mt) cc_final: 0.8349 (mm) REVERT: C 58 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8402 (tp) REVERT: C 136 SER cc_start: 0.8995 (m) cc_final: 0.8775 (p) REVERT: C 242 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7669 (t80) REVERT: C 311 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.6958 (pp30) REVERT: D 52 ASP cc_start: 0.8230 (t70) cc_final: 0.7963 (t70) REVERT: D 311 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7326 (pp30) REVERT: E 235 MET cc_start: 0.7473 (tpp) cc_final: 0.7201 (mmm) REVERT: E 311 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7233 (pp30) REVERT: E 417 ASP cc_start: 0.8119 (t0) cc_final: 0.7894 (t0) outliers start: 34 outliers final: 19 residues processed: 161 average time/residue: 0.2977 time to fit residues: 72.1768 Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 268 ILE 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 268 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 58 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 269 VAL 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 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 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 179 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 chunk 10 optimal weight: 0.0270 chunk 33 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.129011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.099724 restraints weight = 19084.223| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.60 r_work: 0.2888 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 17130 Z= 0.098 Angle : 0.475 5.803 23450 Z= 0.238 Chirality : 0.042 0.147 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.206 16.025 2750 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.87 % Allowed : 15.77 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1930 helix: 2.96 (0.18), residues: 790 sheet: -0.98 (0.21), residues: 505 loop : 0.29 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 459 HIS 0.003 0.000 HIS B 323 PHE 0.010 0.001 PHE B 242 TYR 0.015 0.001 TYR C 67 ARG 0.004 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 15) link_NAG-ASN : angle 1.22906 ( 45) link_BETA1-4 : bond 0.00322 ( 10) link_BETA1-4 : angle 1.82853 ( 30) hydrogen bonds : bond 0.03537 ( 900) hydrogen bonds : angle 4.18816 ( 2736) covalent geometry : bond 0.00210 (17105) covalent geometry : angle 0.46763 (23375) *********************** 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 166 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.709 Fit side-chains REVERT: A 235 MET cc_start: 0.7549 (tpp) cc_final: 0.7204 (mmm) REVERT: A 311 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7349 (pp30) REVERT: B 223 TYR cc_start: 0.7673 (m-80) cc_final: 0.7316 (m-80) REVERT: B 311 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7338 (pp30) REVERT: B 320 TRP cc_start: 0.8409 (p-90) cc_final: 0.8176 (p-90) REVERT: B 427 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7861 (tp) REVERT: C 20 LEU cc_start: 0.8377 (mt) cc_final: 0.8081 (mp) REVERT: C 44 ILE cc_start: 0.8541 (mt) cc_final: 0.8293 (mm) REVERT: C 54 LYS cc_start: 0.7856 (tptp) cc_final: 0.7587 (tptt) REVERT: C 103 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: C 136 SER cc_start: 0.8994 (m) cc_final: 0.8744 (p) REVERT: C 242 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7661 (t80) REVERT: C 311 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7009 (pp30) REVERT: D 311 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: E 235 MET cc_start: 0.7413 (tpp) cc_final: 0.7166 (mmm) REVERT: E 311 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7395 (pp30) outliers start: 34 outliers final: 19 residues processed: 160 average time/residue: 0.2979 time to fit residues: 71.8987 Evaluate side-chains 157 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 410 ARG 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 103 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 311 GLN 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 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 188 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.126192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.097286 restraints weight = 19408.176| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.68 r_work: 0.2856 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17130 Z= 0.168 Angle : 0.521 6.000 23450 Z= 0.259 Chirality : 0.044 0.146 2760 Planarity : 0.004 0.036 2820 Dihedral : 4.466 19.527 2750 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.98 % Allowed : 15.82 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1930 helix: 2.77 (0.18), residues: 790 sheet: -1.02 (0.21), residues: 505 loop : 0.12 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 PHE 0.012 0.001 PHE B 242 TYR 0.017 0.001 TYR C 67 ARG 0.005 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 15) link_NAG-ASN : angle 1.48891 ( 45) link_BETA1-4 : bond 0.00190 ( 10) link_BETA1-4 : angle 1.84331 ( 30) hydrogen bonds : bond 0.03817 ( 900) hydrogen bonds : angle 4.29734 ( 2736) covalent geometry : bond 0.00403 (17105) covalent geometry : angle 0.51304 (23375) *********************** 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 170 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.691 Fit side-chains REVERT: A 223 TYR cc_start: 0.7718 (m-80) cc_final: 0.7372 (m-80) REVERT: A 235 MET cc_start: 0.7615 (tpp) cc_final: 0.7254 (mmm) REVERT: A 311 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7277 (pp30) REVERT: B 223 TYR cc_start: 0.7706 (m-80) cc_final: 0.7366 (m-80) REVERT: B 311 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7325 (pp30) REVERT: B 427 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8081 (tt) REVERT: C 44 ILE cc_start: 0.8658 (mt) cc_final: 0.8420 (mm) REVERT: C 54 LYS cc_start: 0.7945 (tptp) cc_final: 0.7675 (tptt) REVERT: C 58 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8482 (tp) REVERT: C 136 SER cc_start: 0.9025 (m) cc_final: 0.8811 (p) REVERT: C 242 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7754 (t80) REVERT: C 311 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7078 (pp30) REVERT: D 311 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7309 (pp30) REVERT: D 454 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7054 (p) REVERT: E 235 MET cc_start: 0.7482 (tpp) cc_final: 0.7215 (mmm) REVERT: E 311 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7391 (pp30) outliers start: 36 outliers final: 22 residues processed: 161 average time/residue: 0.2859 time to fit residues: 69.7281 Evaluate side-chains 162 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 268 ILE 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 268 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 58 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 269 VAL 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 250 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 250 GLU 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 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 10.0000 chunk 65 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 136 optimal weight: 0.0470 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.5686 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.128190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.100687 restraints weight = 19318.946| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.61 r_work: 0.2871 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1459 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= 0.104 Angle : 0.484 6.114 23450 Z= 0.242 Chirality : 0.042 0.144 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.275 16.523 2750 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.76 % Allowed : 16.26 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1930 helix: 2.92 (0.18), residues: 790 sheet: -0.97 (0.21), residues: 505 loop : 0.28 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 459 HIS 0.004 0.001 HIS B 323 PHE 0.010 0.001 PHE B 242 TYR 0.016 0.001 TYR D 64 ARG 0.007 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 15) link_NAG-ASN : angle 1.28035 ( 45) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.79864 ( 30) hydrogen bonds : bond 0.03583 ( 900) hydrogen bonds : angle 4.21368 ( 2736) covalent geometry : bond 0.00230 (17105) covalent geometry : angle 0.47760 (23375) ********************** 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 166 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.873 Fit side-chains REVERT: A 235 MET cc_start: 0.7654 (tpp) cc_final: 0.7305 (mmm) REVERT: A 311 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7312 (pp30) REVERT: B 223 TYR cc_start: 0.7746 (m-80) cc_final: 0.7388 (m-80) REVERT: B 311 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7350 (pp30) REVERT: B 427 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7937 (tp) REVERT: C 20 LEU cc_start: 0.8509 (mt) cc_final: 0.8192 (mp) REVERT: C 44 ILE cc_start: 0.8564 (mt) cc_final: 0.8327 (mm) REVERT: C 54 LYS cc_start: 0.7980 (tptp) cc_final: 0.7698 (tptt) REVERT: C 103 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8262 (m-10) REVERT: C 136 SER cc_start: 0.8981 (m) cc_final: 0.8779 (p) REVERT: C 242 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7753 (t80) REVERT: C 311 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7048 (pp30) REVERT: D 311 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7345 (pp30) REVERT: E 235 MET cc_start: 0.7538 (tpp) cc_final: 0.7287 (mmm) REVERT: E 311 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7507 (pp30) outliers start: 32 outliers final: 22 residues processed: 158 average time/residue: 0.2922 time to fit residues: 69.5996 Evaluate side-chains 162 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 268 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 410 ARG 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 103 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 269 VAL 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 250 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 311 GLN 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 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.5823 > 50: distance: 58 - 82: 18.324 distance: 68 - 90: 25.227 distance: 74 - 97: 25.903 distance: 78 - 82: 17.376 distance: 82 - 83: 22.864 distance: 83 - 84: 16.389 distance: 83 - 86: 35.667 distance: 84 - 85: 18.143 distance: 84 - 90: 23.466 distance: 86 - 87: 33.417 distance: 87 - 88: 12.053 distance: 87 - 89: 7.727 distance: 90 - 91: 10.441 distance: 91 - 92: 13.578 distance: 91 - 94: 22.379 distance: 92 - 93: 28.006 distance: 92 - 97: 32.946 distance: 94 - 95: 7.660 distance: 94 - 96: 36.123 distance: 97 - 98: 4.078 distance: 98 - 99: 4.406 distance: 98 - 101: 9.796 distance: 99 - 100: 7.701 distance: 99 - 107: 4.646 distance: 101 - 102: 10.015 distance: 102 - 103: 9.241 distance: 102 - 104: 19.506 distance: 103 - 105: 15.947 distance: 104 - 106: 9.650 distance: 105 - 106: 14.846 distance: 107 - 108: 10.654 distance: 108 - 109: 11.519 distance: 108 - 111: 5.759 distance: 109 - 110: 26.474 distance: 109 - 116: 19.106 distance: 111 - 112: 5.891 distance: 112 - 113: 9.430 distance: 113 - 114: 9.603 distance: 114 - 115: 15.817 distance: 116 - 117: 10.401 distance: 117 - 118: 20.004 distance: 117 - 120: 21.780 distance: 118 - 119: 31.275 distance: 118 - 125: 12.964 distance: 120 - 121: 13.871 distance: 121 - 122: 10.838 distance: 122 - 123: 10.802 distance: 122 - 124: 18.433 distance: 125 - 126: 24.997 distance: 126 - 127: 14.885 distance: 126 - 129: 34.575 distance: 127 - 128: 37.115 distance: 127 - 133: 19.089 distance: 129 - 130: 25.396 distance: 130 - 131: 19.659 distance: 130 - 132: 29.540 distance: 133 - 134: 34.200 distance: 134 - 135: 10.234 distance: 134 - 137: 21.623 distance: 135 - 136: 42.382 distance: 135 - 141: 40.128 distance: 138 - 139: 42.296 distance: 138 - 140: 38.449 distance: 141 - 142: 20.918 distance: 142 - 143: 42.839 distance: 142 - 145: 18.485 distance: 143 - 144: 37.072 distance: 143 - 150: 21.600 distance: 145 - 146: 15.615 distance: 146 - 147: 15.211 distance: 147 - 149: 18.164 distance: 150 - 151: 13.587 distance: 151 - 152: 22.077 distance: 151 - 154: 10.410 distance: 152 - 153: 36.207 distance: 152 - 161: 20.042 distance: 154 - 155: 27.855 distance: 155 - 156: 6.275 distance: 156 - 157: 17.807 distance: 157 - 158: 29.286 distance: 158 - 159: 13.820 distance: 158 - 160: 25.543 distance: 161 - 162: 26.918 distance: 162 - 163: 46.807 distance: 162 - 165: 34.534 distance: 163 - 164: 9.934 distance: 163 - 168: 30.332 distance: 165 - 166: 18.114 distance: 166 - 167: 35.174