Starting phenix.real_space_refine on Tue Dec 31 20:28:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cc6_16555/12_2024/8cc6_16555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cc6_16555/12_2024/8cc6_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_16555/12_2024/8cc6_16555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cc6_16555/12_2024/8cc6_16555.map" model { file = "/net/cci-nas-00/data/ceres_data/8cc6_16555/12_2024/8cc6_16555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cc6_16555/12_2024/8cc6_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.42, per 1000 atoms: 0.63 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: 4.43 Conformation dependent library (CDL) restraints added in 2.1 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: 1.71 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: 5.71 Time building geometry restraints manager: 5.10 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: 0.00 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: 1.150 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.850 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.660 ------------------------------------------------------------------------------- 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 17105 Z= 0.241 Angle : 0.601 11.936 23375 Z= 0.309 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 *********************** 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 : 1.879 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: 0.3181 time to fit residues: 66.2015 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 : 1.678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 17105 Z= 0.247 Angle : 0.530 6.401 23375 Z= 0.270 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 *********************** 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 : 1.857 Fit side-chains REVERT: A 235 MET cc_start: 0.7666 (tpp) cc_final: 0.7299 (mmm) REVERT: A 242 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8395 (t80) REVERT: B 417 ASP cc_start: 0.8034 (t0) cc_final: 0.7794 (t0) REVERT: C 50 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8372 (t0) REVERT: C 210 MET cc_start: 0.9029 (tpt) cc_final: 0.8804 (tpt) REVERT: C 235 MET cc_start: 0.7513 (tpp) cc_final: 0.7211 (mmm) REVERT: C 242 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7759 (t80) REVERT: C 415 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8036 (ttpt) REVERT: D 136 SER cc_start: 0.8755 (m) cc_final: 0.8490 (p) REVERT: E 235 MET cc_start: 0.7718 (tpp) cc_final: 0.7381 (mmm) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 0.3093 time to fit residues: 67.2562 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 : 1.939 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 177 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17105 Z= 0.245 Angle : 0.513 6.334 23375 Z= 0.261 Chirality : 0.043 0.139 2760 Planarity : 0.004 0.033 2820 Dihedral : 5.160 42.721 2750 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.48 % Allowed : 14.07 % Favored : 84.45 % 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: 1.25 (0.19), residues: 1930 helix: 2.72 (0.18), residues: 790 sheet: -1.14 (0.20), residues: 505 loop : 0.24 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 459 HIS 0.003 0.001 HIS C 323 PHE 0.011 0.001 PHE B 242 TYR 0.018 0.001 TYR C 67 ARG 0.004 0.000 ARG D 315 *********************** 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 165 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.888 Fit side-chains REVERT: A 136 SER cc_start: 0.8781 (m) cc_final: 0.8554 (p) REVERT: A 235 MET cc_start: 0.7623 (tpp) cc_final: 0.7227 (mmm) REVERT: A 311 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7200 (pp30) REVERT: B 311 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7281 (pp30) REVERT: C 44 ILE cc_start: 0.8737 (mt) cc_final: 0.8456 (mm) REVERT: C 242 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7699 (t80) REVERT: C 311 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7314 (pp30) REVERT: C 415 LYS cc_start: 0.8312 (ttpt) cc_final: 0.8039 (ttpt) REVERT: D 136 SER cc_start: 0.8777 (m) cc_final: 0.8547 (p) REVERT: D 311 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7415 (pp30) REVERT: D 427 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8138 (tt) REVERT: E 235 MET cc_start: 0.7653 (tpp) cc_final: 0.7388 (mmm) REVERT: E 311 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7170 (pp30) REVERT: E 417 ASP cc_start: 0.8094 (t0) cc_final: 0.7885 (t0) outliers start: 27 outliers final: 11 residues processed: 155 average time/residue: 0.3175 time to fit residues: 73.2759 Evaluate side-chains 151 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 410 ARG 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 445 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17105 Z= 0.306 Angle : 0.540 6.470 23375 Z= 0.273 Chirality : 0.044 0.150 2760 Planarity : 0.004 0.035 2820 Dihedral : 5.172 41.062 2750 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.98 % Allowed : 14.89 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.19), residues: 1930 helix: 2.65 (0.18), residues: 790 sheet: -1.25 (0.21), residues: 480 loop : 0.03 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 459 HIS 0.004 0.001 HIS D 323 PHE 0.009 0.001 PHE A 242 TYR 0.018 0.002 TYR D 64 ARG 0.005 0.000 ARG D 315 *********************** 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 175 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 2.046 Fit side-chains REVERT: A 136 SER cc_start: 0.8811 (m) cc_final: 0.8610 (p) REVERT: A 311 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7243 (pp30) REVERT: B 311 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7286 (pp30) REVERT: B 427 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8058 (tt) REVERT: C 44 ILE cc_start: 0.8829 (mt) cc_final: 0.8534 (mm) REVERT: C 50 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8494 (t0) REVERT: C 242 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7658 (t80) REVERT: C 311 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7287 (pp30) REVERT: C 415 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8035 (ttpt) REVERT: D 311 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.7396 (pp30) REVERT: D 427 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8130 (tt) REVERT: E 235 MET cc_start: 0.7565 (tpp) cc_final: 0.7258 (mmm) REVERT: E 311 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: E 417 ASP cc_start: 0.8123 (t0) cc_final: 0.7875 (t0) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.3040 time to fit residues: 76.8711 Evaluate side-chains 158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 427 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 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 221 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 47 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17105 Z= 0.149 Angle : 0.484 7.038 23375 Z= 0.244 Chirality : 0.042 0.205 2760 Planarity : 0.004 0.031 2820 Dihedral : 4.651 31.690 2750 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.76 % Allowed : 15.00 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.38 (0.20), residues: 1930 helix: 2.89 (0.18), residues: 790 sheet: -1.08 (0.21), residues: 505 loop : 0.21 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 459 HIS 0.003 0.001 HIS D 323 PHE 0.009 0.001 PHE B 242 TYR 0.016 0.001 TYR D 64 ARG 0.005 0.000 ARG C 315 *********************** 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 173 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.828 Fit side-chains REVERT: A 136 SER cc_start: 0.8792 (m) cc_final: 0.8576 (p) REVERT: A 235 MET cc_start: 0.7515 (tpp) cc_final: 0.7127 (mmm) REVERT: A 311 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7290 (pp30) REVERT: B 311 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7345 (pp30) REVERT: B 427 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7880 (tp) REVERT: C 44 ILE cc_start: 0.8707 (mt) cc_final: 0.8431 (mm) REVERT: C 50 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8482 (t0) REVERT: C 242 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7629 (t80) REVERT: C 311 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7067 (pp30) REVERT: D 311 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7431 (pp30) REVERT: D 427 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8137 (tt) REVERT: E 235 MET cc_start: 0.7510 (tpp) cc_final: 0.7224 (mmm) REVERT: E 242 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7123 (t80) REVERT: E 311 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7238 (pp30) REVERT: E 417 ASP cc_start: 0.8087 (t0) cc_final: 0.7832 (t0) REVERT: E 427 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8067 (tp) outliers start: 32 outliers final: 14 residues processed: 165 average time/residue: 0.3135 time to fit residues: 77.3137 Evaluate side-chains 161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 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 221 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 410 ARG Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17105 Z= 0.174 Angle : 0.483 5.816 23375 Z= 0.243 Chirality : 0.042 0.164 2760 Planarity : 0.004 0.032 2820 Dihedral : 4.473 23.933 2750 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.36 % Allowed : 14.84 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.20), residues: 1930 helix: 2.86 (0.18), residues: 790 sheet: -1.02 (0.21), residues: 505 loop : 0.24 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 459 HIS 0.004 0.001 HIS D 323 PHE 0.009 0.001 PHE A 254 TYR 0.016 0.001 TYR A 67 ARG 0.005 0.000 ARG C 315 *********************** 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 178 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 1.961 Fit side-chains REVERT: A 136 SER cc_start: 0.8798 (m) cc_final: 0.8587 (p) REVERT: A 235 MET cc_start: 0.7494 (tpp) cc_final: 0.7128 (mmm) REVERT: A 311 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7330 (pp30) REVERT: B 311 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7291 (pp30) REVERT: B 427 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7935 (tp) REVERT: C 44 ILE cc_start: 0.8734 (mt) cc_final: 0.8465 (mm) REVERT: C 50 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8529 (t0) REVERT: C 242 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7613 (t80) REVERT: C 311 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7129 (pp30) REVERT: D 311 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7411 (pp30) REVERT: D 427 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8082 (tt) REVERT: E 235 MET cc_start: 0.7516 (tpp) cc_final: 0.7220 (mmm) REVERT: E 242 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7103 (t80) REVERT: E 311 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7305 (pp30) REVERT: E 417 ASP cc_start: 0.8080 (t0) cc_final: 0.7829 (t0) REVERT: E 427 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8063 (tp) outliers start: 43 outliers final: 22 residues processed: 169 average time/residue: 0.3150 time to fit residues: 80.4903 Evaluate side-chains 165 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 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 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 269 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 410 ARG Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17105 Z= 0.221 Angle : 0.500 5.868 23375 Z= 0.251 Chirality : 0.043 0.149 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.490 19.239 2750 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.25 % Allowed : 15.16 % Favored : 82.58 % 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: 1.33 (0.20), residues: 1930 helix: 2.80 (0.18), residues: 790 sheet: -1.02 (0.21), residues: 505 loop : 0.17 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 459 HIS 0.004 0.001 HIS D 323 PHE 0.010 0.001 PHE D 242 TYR 0.017 0.001 TYR D 64 ARG 0.006 0.000 ARG C 315 *********************** 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 179 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 1.861 Fit side-chains REVERT: A 235 MET cc_start: 0.7519 (tpp) cc_final: 0.7153 (mmm) REVERT: A 311 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7329 (pp30) REVERT: B 223 TYR cc_start: 0.7829 (m-80) cc_final: 0.7538 (m-80) REVERT: B 311 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.7321 (pp30) REVERT: B 427 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8060 (tt) REVERT: C 44 ILE cc_start: 0.8781 (mt) cc_final: 0.8512 (mm) REVERT: C 50 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8514 (t0) REVERT: C 242 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7668 (t80) REVERT: C 311 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7147 (pp30) REVERT: D 311 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7412 (pp30) REVERT: D 427 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (tt) REVERT: D 454 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7383 (p) REVERT: E 235 MET cc_start: 0.7432 (tpp) cc_final: 0.7147 (mmm) REVERT: E 311 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7436 (pp30) REVERT: E 417 ASP cc_start: 0.8081 (t0) cc_final: 0.7842 (t0) REVERT: E 427 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8061 (tp) outliers start: 41 outliers final: 24 residues processed: 169 average time/residue: 0.3169 time to fit residues: 81.4168 Evaluate side-chains 171 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 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 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 250 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17105 Z= 0.263 Angle : 0.519 6.150 23375 Z= 0.260 Chirality : 0.044 0.165 2760 Planarity : 0.004 0.036 2820 Dihedral : 4.575 20.103 2750 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.25 % Allowed : 15.27 % Favored : 82.47 % 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: 2.73 (0.18), residues: 790 sheet: -1.16 (0.21), residues: 480 loop : 0.04 (0.25), residues: 660 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 0.012 0.001 PHE D 242 TYR 0.017 0.001 TYR D 64 ARG 0.006 0.000 ARG C 315 *********************** 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 182 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.798 Fit side-chains REVERT: A 223 TYR cc_start: 0.7896 (m-80) cc_final: 0.7564 (m-80) REVERT: A 235 MET cc_start: 0.7525 (tpp) cc_final: 0.7148 (mmm) REVERT: A 311 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7315 (pp30) REVERT: B 223 TYR cc_start: 0.7831 (m-80) cc_final: 0.7548 (m-80) REVERT: B 311 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7377 (pp30) REVERT: B 427 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8048 (tt) REVERT: C 44 ILE cc_start: 0.8824 (mt) cc_final: 0.8557 (mm) REVERT: C 50 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8513 (t0) REVERT: C 242 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7666 (t80) REVERT: C 311 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7136 (pp30) REVERT: D 311 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7418 (pp30) REVERT: D 427 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8140 (tt) REVERT: D 454 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7380 (p) REVERT: E 235 MET cc_start: 0.7447 (tpp) cc_final: 0.7161 (mmm) REVERT: E 311 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7298 (pp30) REVERT: E 417 ASP cc_start: 0.8096 (t0) cc_final: 0.7876 (t0) REVERT: E 427 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8062 (tp) outliers start: 41 outliers final: 25 residues processed: 172 average time/residue: 0.3145 time to fit residues: 81.6869 Evaluate side-chains 172 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 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 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 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 250 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 ILE 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 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17105 Z= 0.161 Angle : 0.481 5.834 23375 Z= 0.243 Chirality : 0.042 0.157 2760 Planarity : 0.004 0.033 2820 Dihedral : 4.331 16.634 2750 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.81 % Allowed : 15.77 % Favored : 82.42 % 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: 1.46 (0.20), residues: 1930 helix: 2.92 (0.18), residues: 790 sheet: -1.01 (0.21), residues: 505 loop : 0.27 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 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 0.006 0.000 ARG C 315 *********************** 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 173 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.832 Fit side-chains REVERT: A 235 MET cc_start: 0.7508 (tpp) cc_final: 0.7147 (mmm) REVERT: A 311 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7303 (pp30) REVERT: B 223 TYR cc_start: 0.7774 (m-80) cc_final: 0.7452 (m-80) REVERT: B 311 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7375 (pp30) REVERT: B 427 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 20 LEU cc_start: 0.8641 (mt) cc_final: 0.8389 (mp) REVERT: C 44 ILE cc_start: 0.8723 (mt) cc_final: 0.8471 (mm) REVERT: C 50 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8528 (t0) REVERT: C 54 LYS cc_start: 0.7929 (tptp) cc_final: 0.7674 (tptt) REVERT: C 242 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7614 (t80) REVERT: C 311 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7132 (pp30) REVERT: D 311 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7392 (pp30) REVERT: D 427 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8150 (tt) REVERT: E 235 MET cc_start: 0.7410 (tpp) cc_final: 0.7135 (mmm) REVERT: E 311 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7366 (pp30) REVERT: E 427 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8062 (tp) outliers start: 33 outliers final: 21 residues processed: 164 average time/residue: 0.3056 time to fit residues: 75.7781 Evaluate side-chains 170 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 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 D residue 221 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 ILE 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 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 178 optimal weight: 0.0020 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17105 Z= 0.196 Angle : 0.491 6.015 23375 Z= 0.247 Chirality : 0.043 0.159 2760 Planarity : 0.004 0.035 2820 Dihedral : 4.350 18.010 2750 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.87 % Allowed : 16.10 % Favored : 82.03 % 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: 1.41 (0.20), residues: 1930 helix: 2.85 (0.18), residues: 790 sheet: -1.00 (0.21), residues: 505 loop : 0.26 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 459 HIS 0.004 0.001 HIS D 323 PHE 0.010 0.001 PHE B 242 TYR 0.016 0.001 TYR D 64 ARG 0.006 0.000 ARG C 315 ********************** 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 167 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.873 Fit side-chains REVERT: A 235 MET cc_start: 0.7517 (tpp) cc_final: 0.7155 (mmm) REVERT: A 311 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7314 (pp30) REVERT: B 223 TYR cc_start: 0.7756 (m-80) cc_final: 0.7408 (m-80) REVERT: B 311 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7367 (pp30) REVERT: B 427 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7934 (tp) REVERT: C 44 ILE cc_start: 0.8753 (mt) cc_final: 0.8486 (mm) REVERT: C 50 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8537 (t0) REVERT: C 54 LYS cc_start: 0.7966 (tptp) cc_final: 0.7700 (tptt) REVERT: C 242 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7660 (t80) REVERT: C 311 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7134 (pp30) REVERT: D 311 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7399 (pp30) REVERT: D 427 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8081 (tt) REVERT: E 235 MET cc_start: 0.7414 (tpp) cc_final: 0.7137 (mmm) REVERT: E 311 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7414 (pp30) REVERT: E 427 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8057 (tp) outliers start: 34 outliers final: 24 residues processed: 158 average time/residue: 0.3059 time to fit residues: 73.2270 Evaluate side-chains 167 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 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 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 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 242 PHE 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 427 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 ILE 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 427 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.7980 chunk 47 optimal weight: 0.0070 chunk 142 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- 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 = 0.127270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099083 restraints weight = 19306.773| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.66 r_work: 0.2859 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17105 Z= 0.203 Angle : 0.493 5.839 23375 Z= 0.248 Chirality : 0.043 0.160 2760 Planarity : 0.004 0.034 2820 Dihedral : 4.369 18.309 2750 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.98 % Allowed : 16.04 % 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: 1.39 (0.20), residues: 1930 helix: 2.85 (0.18), residues: 790 sheet: -1.01 (0.21), residues: 505 loop : 0.24 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 459 HIS 0.004 0.001 HIS D 323 PHE 0.010 0.001 PHE B 242 TYR 0.016 0.001 TYR D 64 ARG 0.006 0.000 ARG C 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2923.09 seconds wall clock time: 55 minutes 3.30 seconds (3303.30 seconds total)