Starting phenix.real_space_refine on Thu Aug 6 01:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qud_18660/08_2026/8qud_18660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qud_18660/08_2026/8qud_18660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qud_18660/08_2026/8qud_18660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qud_18660/08_2026/8qud_18660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qud_18660/08_2026/8qud_18660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qud_18660/08_2026/8qud_18660.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 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: 7 Type Number sf(0) Gaussians K 6 8.98 5 Zn 4 6.06 5 P 4 5.49 5 S 68 5.16 5 C 8372 2.51 5 N 2060 2.21 5 O 2292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12806 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3065 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 7, 'TRP:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3065 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 7, 'TRP:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "D" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3065 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 7, 'TRP:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3065 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 7, 'TRP:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 111 Unusual residues: {' K': 3, ' ZN': 1, 'PCF': 1, 'WY0': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Unusual residues: {' K': 1, ' ZN': 1, 'PCF': 1, 'WY0': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {' ZN': 1, 'PCF': 1, 'WY0': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 110 Unusual residues: {' K': 2, ' ZN': 1, 'PCF': 1, 'WY0': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 792 SG CYS A 104 64.055 44.023 43.767 1.00 15.48 S ATOM 798 SG CYS A 105 60.803 45.874 42.921 1.00 8.94 S ATOM 3688 SG CYS B 83 64.063 46.949 41.212 1.00 10.97 S ATOM 3857 SG CYS B 104 69.817 63.997 43.781 1.00 15.48 S ATOM 3863 SG CYS B 105 67.968 60.743 42.940 1.00 8.94 S ATOM 9818 SG CYS C 83 67.001 64.066 41.210 1.00 10.97 S ATOM 623 SG CYS A 83 47.014 49.789 41.174 1.00 10.97 S ATOM 6922 SG CYS D 104 44.074 49.854 43.792 1.00 15.48 S ATOM 6928 SG CYS D 105 45.917 53.110 42.947 1.00 8.94 S ATOM 6753 SG CYS D 83 49.802 66.909 41.208 1.00 10.97 S ATOM 9987 SG CYS C 104 49.937 69.775 43.771 1.00 15.48 S ATOM 9993 SG CYS C 105 53.196 67.935 42.931 1.00 8.94 S Time building chain proxies: 3.31, per 1000 atoms: 0.26 Number of scatterers: 12806 At special positions: 0 Unit cell: (114.675, 114.675, 121.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 6 19.00 S 68 16.00 P 4 15.00 O 2292 8.00 N 2060 7.00 C 8372 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 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 579.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 602 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 105 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 602 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 105 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 603 " - pdb=" SG CYS D 83 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 603 " - pdb=" SG CYS A 83 " Number of angles added : 12 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2984 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 75.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.851A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.675A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 4.640A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N HIS A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 210 Processing helix chain 'A' and resid 211 through 216 removed outlier: 6.375A pdb=" N ARG A 214 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 266 removed outlier: 3.879A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 276 through 297 Proline residue: A 288 - end of helix removed outlier: 4.153A pdb=" N GLY A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.929A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 375 through 382 removed outlier: 3.693A pdb=" N SER A 379 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS A 381 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 382 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.695A pdb=" N TRP A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.850A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.675A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 4.640A pdb=" N MET B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 186 through 210 Processing helix chain 'B' and resid 211 through 216 removed outlier: 6.375A pdb=" N ARG B 214 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.879A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 276 through 297 Proline residue: B 288 - end of helix removed outlier: 4.153A pdb=" N GLY B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 314 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.929A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 375 through 382 removed outlier: 3.693A pdb=" N SER B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS B 381 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 382 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.695A pdb=" N TRP B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 431 through 452 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.851A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.675A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 4.640A pdb=" N MET D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR D 108 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 182 through 185 Processing helix chain 'D' and resid 186 through 210 Processing helix chain 'D' and resid 211 through 216 removed outlier: 6.375A pdb=" N ARG D 214 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 3.878A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 276 through 297 Proline residue: D 288 - end of helix removed outlier: 4.152A pdb=" N GLY D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 314 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 320 through 325 removed outlier: 3.929A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 375 through 382 removed outlier: 3.693A pdb=" N SER D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR D 382 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.694A pdb=" N TRP D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.851A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.675A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 4.640A pdb=" N MET C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR C 108 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 182 through 185 Processing helix chain 'C' and resid 186 through 210 Processing helix chain 'C' and resid 211 through 216 removed outlier: 6.375A pdb=" N ARG C 214 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 266 removed outlier: 3.879A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 276 through 297 Proline residue: C 288 - end of helix removed outlier: 4.152A pdb=" N GLY C 297 " --> pdb=" O VAL C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.929A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 375 through 382 removed outlier: 3.693A pdb=" N SER C 379 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS C 381 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 382 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.695A pdb=" N TRP C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 218 through 219 Processing sheet with id=AA5, first strand: chain 'D' and resid 17 through 22 Processing sheet with id=AA6, first strand: chain 'D' and resid 218 through 219 Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 22 Processing sheet with id=AA8, first strand: chain 'C' and resid 218 through 219 836 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1936 1.31 - 1.44: 3800 1.44 - 1.56: 7222 1.56 - 1.69: 10 1.69 - 1.81: 104 Bond restraints: 13072 Sorted by residual: bond pdb=" C21 PCF D 601 " pdb=" O21 PCF D 601 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C21 PCF A 604 " pdb=" O21 PCF A 604 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C21 PCF C 601 " pdb=" O21 PCF C 601 " ideal model delta sigma weight residual 1.334 1.426 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C21 PCF B 604 " pdb=" O21 PCF B 604 " ideal model delta sigma weight residual 1.334 1.425 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C31 PCF A 604 " pdb=" O31 PCF A 604 " ideal model delta sigma weight residual 1.329 1.417 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 13067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 17569 2.84 - 5.68: 271 5.68 - 8.52: 5 8.52 - 11.35: 7 11.35 - 14.19: 4 Bond angle restraints: 17856 Sorted by residual: angle pdb=" O12 PCF B 604 " pdb=" P PCF B 604 " pdb=" O14 PCF B 604 " ideal model delta sigma weight residual 123.69 109.50 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" O12 PCF D 601 " pdb=" P PCF D 601 " pdb=" O14 PCF D 601 " ideal model delta sigma weight residual 123.69 109.50 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" O12 PCF A 604 " pdb=" P PCF A 604 " pdb=" O14 PCF A 604 " ideal model delta sigma weight residual 123.69 109.51 14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O12 PCF C 601 " pdb=" P PCF C 601 " pdb=" O14 PCF C 601 " ideal model delta sigma weight residual 123.69 109.52 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C22 PCF A 604 " pdb=" C21 PCF A 604 " pdb=" O21 PCF A 604 " ideal model delta sigma weight residual 111.13 120.02 -8.89 3.00e+00 1.11e-01 8.79e+00 ... (remaining 17851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 6721 17.34 - 34.68: 782 34.68 - 52.02: 313 52.02 - 69.36: 36 69.36 - 86.71: 12 Dihedral angle restraints: 7864 sinusoidal: 3260 harmonic: 4604 Sorted by residual: dihedral pdb=" CB GLU D 102 " pdb=" CG GLU D 102 " pdb=" CD GLU D 102 " pdb=" OE1 GLU D 102 " ideal model delta sinusoidal sigma weight residual 0.00 -86.71 86.71 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU B 102 " pdb=" CG GLU B 102 " pdb=" CD GLU B 102 " pdb=" OE1 GLU B 102 " ideal model delta sinusoidal sigma weight residual 0.00 -86.70 86.70 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU C 102 " pdb=" CG GLU C 102 " pdb=" CD GLU C 102 " pdb=" OE1 GLU C 102 " ideal model delta sinusoidal sigma weight residual 0.00 -86.70 86.70 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 7861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1134 0.025 - 0.050: 563 0.050 - 0.075: 174 0.075 - 0.100: 76 0.100 - 0.124: 45 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CA ILE B 460 " pdb=" N ILE B 460 " pdb=" C ILE B 460 " pdb=" CB ILE B 460 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 460 " pdb=" N ILE A 460 " pdb=" C ILE A 460 " pdb=" CB ILE A 460 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE D 460 " pdb=" N ILE D 460 " pdb=" C ILE D 460 " pdb=" CB ILE D 460 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1989 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 WY0 C 602 " 0.085 2.00e-02 2.50e+03 5.88e-02 6.91e+01 pdb=" C16 WY0 C 602 " -0.017 2.00e-02 2.50e+03 pdb=" C17 WY0 C 602 " 0.072 2.00e-02 2.50e+03 pdb=" C18 WY0 C 602 " -0.014 2.00e-02 2.50e+03 pdb=" N2 WY0 C 602 " 0.017 2.00e-02 2.50e+03 pdb=" N3 WY0 C 602 " 0.024 2.00e-02 2.50e+03 pdb=" O3 WY0 C 602 " -0.091 2.00e-02 2.50e+03 pdb=" O4 WY0 C 602 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 WY0 A 601 " -0.085 2.00e-02 2.50e+03 5.87e-02 6.89e+01 pdb=" C16 WY0 A 601 " 0.017 2.00e-02 2.50e+03 pdb=" C17 WY0 A 601 " -0.072 2.00e-02 2.50e+03 pdb=" C18 WY0 A 601 " 0.014 2.00e-02 2.50e+03 pdb=" N2 WY0 A 601 " -0.016 2.00e-02 2.50e+03 pdb=" N3 WY0 A 601 " -0.024 2.00e-02 2.50e+03 pdb=" O3 WY0 A 601 " 0.091 2.00e-02 2.50e+03 pdb=" O4 WY0 A 601 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 WY0 D 602 " -0.085 2.00e-02 2.50e+03 5.87e-02 6.88e+01 pdb=" C16 WY0 D 602 " 0.017 2.00e-02 2.50e+03 pdb=" C17 WY0 D 602 " -0.072 2.00e-02 2.50e+03 pdb=" C18 WY0 D 602 " 0.014 2.00e-02 2.50e+03 pdb=" N2 WY0 D 602 " -0.016 2.00e-02 2.50e+03 pdb=" N3 WY0 D 602 " -0.024 2.00e-02 2.50e+03 pdb=" O3 WY0 D 602 " 0.091 2.00e-02 2.50e+03 pdb=" O4 WY0 D 602 " 0.075 2.00e-02 2.50e+03 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 352 2.71 - 3.32: 15619 3.32 - 3.93: 26593 3.93 - 4.53: 36843 4.53 - 5.14: 52886 Nonbonded interactions: 132293 Sorted by model distance: nonbonded pdb=" O THR B 25 " pdb=" OG1 THR B 28 " model vdw 2.103 3.040 nonbonded pdb=" O THR A 25 " pdb=" OG1 THR A 28 " model vdw 2.103 3.040 nonbonded pdb=" O THR C 25 " pdb=" OG1 THR C 28 " model vdw 2.103 3.040 nonbonded pdb=" O THR D 25 " pdb=" OG1 THR D 28 " model vdw 2.104 3.040 nonbonded pdb=" O ARG A 311 " pdb=" NH1 ARG A 311 " model vdw 2.153 3.120 ... (remaining 132288 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 7 through 463) selection = (chain 'B' and resid 7 through 463) selection = (chain 'C' and resid 7 through 463) selection = (chain 'D' and resid 7 through 463) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.040 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.005 0.093 13088 Z= 0.243 Angle : 0.743 14.193 17868 Z= 0.346 Chirality : 0.037 0.124 1992 Planarity : 0.006 0.059 2212 Dihedral : 17.333 86.705 4880 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.49 % Allowed : 22.17 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.22), residues: 1556 helix: 1.66 (0.17), residues: 1024 sheet: -4.14 (0.57), residues: 48 loop : 1.27 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 311 TYR 0.005 0.001 TYR B 365 PHE 0.009 0.001 PHE B 384 TRP 0.013 0.001 TRP C 411 HIS 0.002 0.000 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.24 (13072) covalent geometry : angle 0.74239 / 0.35 (17856) hydrogen bonds : bond 0.12285 / 8.32 ( 836) hydrogen bonds : angle 5.08239 / 3.69 ( 2376) metal coordination : bond 0.02091 / 1.05 ( 16) metal coordination : angle 1.55097 / 0.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.486 Fit side-chains REVERT: A 314 ARG cc_start: 0.7293 (ttm170) cc_final: 0.6367 (tpm-80) REVERT: B 314 ARG cc_start: 0.7225 (ttm170) cc_final: 0.6312 (tpm-80) REVERT: D 314 ARG cc_start: 0.7396 (ttm170) cc_final: 0.6439 (tpm-80) REVERT: C 311 ARG cc_start: 0.5415 (tpt90) cc_final: 0.5158 (tpt90) REVERT: C 314 ARG cc_start: 0.7211 (ttm170) cc_final: 0.6217 (tpm-80) outliers start: 6 outliers final: 1 residues processed: 149 average time/residue: 0.7055 time to fit residues: 113.7170 Evaluate side-chains 144 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 276 ASN A 438 ASN A 450 GLN B 66 HIS B 111 GLN B 276 ASN B 438 ASN B 450 GLN D 66 HIS D 111 GLN D 276 ASN D 438 ASN D 450 GLN C 60 HIS C 66 HIS C 111 GLN C 276 ASN C 438 ASN C 450 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.218351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159350 restraints weight = 11242.520| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.20 r_work: 0.3551 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13088 Z= 0.207 Angle : 0.635 5.166 17868 Z= 0.333 Chirality : 0.043 0.185 1992 Planarity : 0.006 0.053 2212 Dihedral : 11.224 59.901 2286 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.64 % Allowed : 18.61 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1556 helix: 1.20 (0.16), residues: 1056 sheet: -3.72 (0.63), residues: 48 loop : 1.10 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.010 0.002 TYR B 407 PHE 0.016 0.002 PHE D 384 TRP 0.011 0.002 TRP C 392 HIS 0.007 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (13072) covalent geometry : angle 0.63298 / 0.33 (17856) hydrogen bonds : bond 0.06839 / 4.70 ( 836) hydrogen bonds : angle 4.76313 / 3.43 ( 2376) metal coordination : bond 0.01198 / 0.75 ( 16) metal coordination : angle 2.23450 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.400 Fit side-chains REVERT: C 89 GLU cc_start: 0.7802 (tp30) cc_final: 0.6885 (mt-10) REVERT: C 441 MET cc_start: 0.8301 (mtt) cc_final: 0.8087 (mtt) REVERT: C 458 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6776 (ttmt) outliers start: 45 outliers final: 13 residues processed: 170 average time/residue: 0.6424 time to fit residues: 118.2116 Evaluate side-chains 156 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 450 GLN Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 ASN ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 ASN ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.214435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.170960 restraints weight = 11288.247| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.30 r_work: 0.3456 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 13088 Z= 0.298 Angle : 0.737 6.190 17868 Z= 0.389 Chirality : 0.050 0.193 1992 Planarity : 0.007 0.055 2212 Dihedral : 11.461 57.324 2284 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.83 % Allowed : 16.59 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1556 helix: 0.85 (0.16), residues: 1048 sheet: -3.67 (0.66), residues: 48 loop : 0.78 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 72 TYR 0.013 0.003 TYR B 407 PHE 0.019 0.003 PHE A 384 TRP 0.015 0.003 TRP C 94 HIS 0.009 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (13072) covalent geometry : angle 0.73376 / 0.39 (17856) hydrogen bonds : bond 0.07979 / 5.46 ( 836) hydrogen bonds : angle 5.06920 / 3.64 ( 2376) metal coordination : bond 0.01009 / 0.63 ( 16) metal coordination : angle 2.79748 / 1.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 133 time to evaluate : 0.494 Fit side-chains REVERT: A 201 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6120 (mp) REVERT: B 201 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6084 (mp) REVERT: D 89 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: D 201 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6120 (mp) REVERT: C 201 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6138 (mp) outliers start: 72 outliers final: 31 residues processed: 183 average time/residue: 0.5838 time to fit residues: 116.4384 Evaluate side-chains 163 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 450 GLN D 450 GLN C 216 ASN C 450 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.218385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161708 restraints weight = 11322.687| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.21 r_work: 0.3559 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13088 Z= 0.162 Angle : 0.586 5.407 17868 Z= 0.305 Chirality : 0.041 0.133 1992 Planarity : 0.005 0.052 2212 Dihedral : 10.814 58.111 2284 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.72 % Allowed : 18.61 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1556 helix: 1.13 (0.16), residues: 1052 sheet: -3.40 (0.66), residues: 48 loop : 0.90 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.008 0.001 TYR B 365 PHE 0.015 0.002 PHE C 384 TRP 0.010 0.002 TRP B 94 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (13072) covalent geometry : angle 0.58441 / 0.30 (17856) hydrogen bonds : bond 0.06020 / 4.15 ( 836) hydrogen bonds : angle 4.68509 / 3.37 ( 2376) metal coordination : bond 0.00677 / 0.43 ( 16) metal coordination : angle 1.69889 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.284 Fit side-chains REVERT: A 89 GLU cc_start: 0.7801 (tp30) cc_final: 0.6869 (mt-10) REVERT: A 201 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6166 (mp) REVERT: B 89 GLU cc_start: 0.7795 (tp30) cc_final: 0.6863 (mt-10) REVERT: B 201 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6168 (mp) REVERT: D 89 GLU cc_start: 0.7717 (tp30) cc_final: 0.6788 (mt-10) REVERT: D 201 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6165 (mp) REVERT: C 89 GLU cc_start: 0.7752 (tp30) cc_final: 0.6815 (mt-10) REVERT: C 201 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6173 (mp) REVERT: C 458 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6736 (ttmt) outliers start: 46 outliers final: 23 residues processed: 155 average time/residue: 0.5666 time to fit residues: 95.0265 Evaluate side-chains 159 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.215885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.155759 restraints weight = 11290.261| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.23 r_work: 0.3517 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13088 Z= 0.229 Angle : 0.662 5.849 17868 Z= 0.348 Chirality : 0.045 0.147 1992 Planarity : 0.006 0.055 2212 Dihedral : 10.873 59.505 2284 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.85 % Allowed : 18.69 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1556 helix: 0.99 (0.16), residues: 1048 sheet: -3.26 (0.67), residues: 48 loop : 0.75 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.010 0.002 TYR C 407 PHE 0.018 0.002 PHE C 64 TRP 0.013 0.002 TRP D 94 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (13072) covalent geometry : angle 0.65903 / 0.35 (17856) hydrogen bonds : bond 0.07097 / 4.87 ( 836) hydrogen bonds : angle 4.86315 / 3.49 ( 2376) metal coordination : bond 0.00875 / 0.55 ( 16) metal coordination : angle 2.31406 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 122 time to evaluate : 0.329 Fit side-chains REVERT: A 8 GLU cc_start: 0.6760 (tp30) cc_final: 0.6424 (tp30) REVERT: A 201 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6160 (mp) REVERT: B 201 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6152 (mp) REVERT: D 8 GLU cc_start: 0.6767 (tp30) cc_final: 0.6418 (tp30) REVERT: D 201 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6144 (mp) REVERT: C 201 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6142 (mp) REVERT: C 458 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6772 (ttmt) outliers start: 60 outliers final: 34 residues processed: 164 average time/residue: 0.6260 time to fit residues: 111.1445 Evaluate side-chains 157 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.219996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163896 restraints weight = 11289.117| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.18 r_work: 0.3585 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13088 Z= 0.138 Angle : 0.559 6.505 17868 Z= 0.290 Chirality : 0.039 0.128 1992 Planarity : 0.005 0.050 2212 Dihedral : 10.268 59.740 2284 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.64 % Allowed : 19.98 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1556 helix: 1.28 (0.16), residues: 1052 sheet: -2.95 (0.66), residues: 48 loop : 0.93 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.010 0.001 TYR C 48 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.002 TRP C 411 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (13072) covalent geometry : angle 0.55784 / 0.29 (17856) hydrogen bonds : bond 0.05428 / 3.76 ( 836) hydrogen bonds : angle 4.51003 / 3.24 ( 2376) metal coordination : bond 0.00468 / 0.29 ( 16) metal coordination : angle 1.36683 / 0.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.490 Fit side-chains REVERT: A 8 GLU cc_start: 0.6773 (tp30) cc_final: 0.6356 (tp30) REVERT: A 89 GLU cc_start: 0.7619 (tp30) cc_final: 0.6682 (mt-10) REVERT: A 201 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6126 (mp) REVERT: A 406 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8123 (ptm) REVERT: B 89 GLU cc_start: 0.7622 (tp30) cc_final: 0.6702 (mt-10) REVERT: B 201 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6135 (mp) REVERT: B 458 LYS cc_start: 0.6933 (tttt) cc_final: 0.6717 (ttmt) REVERT: D 89 GLU cc_start: 0.7625 (tp30) cc_final: 0.6680 (mt-10) REVERT: D 201 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6114 (mp) REVERT: D 406 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8114 (ptm) REVERT: C 89 GLU cc_start: 0.7611 (tp30) cc_final: 0.6706 (mt-10) REVERT: C 201 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6172 (mp) REVERT: C 406 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8106 (ptm) REVERT: C 458 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6732 (ttmt) outliers start: 45 outliers final: 22 residues processed: 161 average time/residue: 0.6449 time to fit residues: 113.0311 Evaluate side-chains 156 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN A 438 ASN B 386 ASN B 438 ASN D 386 ASN D 438 ASN C 386 ASN C 438 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.214478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.169186 restraints weight = 11185.150| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.06 r_work: 0.3564 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13088 Z= 0.281 Angle : 0.727 7.046 17868 Z= 0.383 Chirality : 0.048 0.155 1992 Planarity : 0.006 0.056 2212 Dihedral : 10.856 54.938 2284 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.02 % Allowed : 19.50 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1556 helix: 0.84 (0.16), residues: 1056 sheet: -3.21 (0.67), residues: 48 loop : 0.77 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 311 TYR 0.014 0.003 TYR C 48 PHE 0.020 0.003 PHE C 64 TRP 0.016 0.003 TRP C 411 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 (13072) covalent geometry : angle 0.72449 / 0.38 (17856) hydrogen bonds : bond 0.07694 / 5.27 ( 836) hydrogen bonds : angle 4.94451 / 3.55 ( 2376) metal coordination : bond 0.00791 / 0.49 ( 16) metal coordination : angle 2.48279 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 127 time to evaluate : 0.488 Fit side-chains REVERT: A 8 GLU cc_start: 0.6881 (tp30) cc_final: 0.6509 (tp30) REVERT: A 201 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6032 (mp) REVERT: B 201 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6035 (mp) REVERT: D 201 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6005 (mp) REVERT: D 422 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8285 (mt) REVERT: C 201 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6044 (mp) outliers start: 62 outliers final: 37 residues processed: 171 average time/residue: 0.6080 time to fit residues: 113.2277 Evaluate side-chains 167 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN B 386 ASN D 386 ASN C 386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.219999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.178927 restraints weight = 11258.948| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.00 r_work: 0.3553 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13088 Z= 0.140 Angle : 0.575 8.271 17868 Z= 0.297 Chirality : 0.039 0.128 1992 Planarity : 0.005 0.050 2212 Dihedral : 10.110 57.498 2284 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.80 % Allowed : 20.63 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.22), residues: 1556 helix: 1.19 (0.16), residues: 1060 sheet: -2.94 (0.65), residues: 48 loop : 1.01 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 311 TYR 0.011 0.001 TYR B 48 PHE 0.012 0.001 PHE C 384 TRP 0.020 0.002 TRP D 411 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (13072) covalent geometry : angle 0.57413 / 0.30 (17856) hydrogen bonds : bond 0.05376 / 3.72 ( 836) hydrogen bonds : angle 4.48656 / 3.22 ( 2376) metal coordination : bond 0.00423 / 0.27 ( 16) metal coordination : angle 1.39838 / 0.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.498 Fit side-chains REVERT: A 8 GLU cc_start: 0.6772 (tp30) cc_final: 0.6302 (tp30) REVERT: A 89 GLU cc_start: 0.7652 (tp30) cc_final: 0.6610 (mt-10) REVERT: A 201 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6095 (mp) REVERT: A 217 PRO cc_start: 0.7348 (Cg_exo) cc_final: 0.7070 (Cg_endo) REVERT: A 406 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8149 (ptm) REVERT: B 89 GLU cc_start: 0.7608 (tp30) cc_final: 0.6586 (mt-10) REVERT: B 201 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6114 (mp) REVERT: B 458 LYS cc_start: 0.6895 (tttt) cc_final: 0.6647 (ttmt) REVERT: D 8 GLU cc_start: 0.6672 (tp30) cc_final: 0.6302 (tp30) REVERT: D 89 GLU cc_start: 0.7648 (tp30) cc_final: 0.6645 (mt-10) REVERT: D 201 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6119 (mp) REVERT: D 217 PRO cc_start: 0.7354 (Cg_exo) cc_final: 0.7081 (Cg_endo) REVERT: D 379 SER cc_start: 0.7587 (p) cc_final: 0.7204 (m) REVERT: D 406 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8145 (ptm) REVERT: C 89 GLU cc_start: 0.7743 (tp30) cc_final: 0.6747 (mt-10) REVERT: C 201 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6129 (mp) REVERT: C 406 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8141 (ptm) REVERT: C 458 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6694 (ttmt) outliers start: 47 outliers final: 24 residues processed: 171 average time/residue: 0.5543 time to fit residues: 103.9377 Evaluate side-chains 160 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 438 ASN B 13 ASN B 438 ASN D 13 ASN D 438 ASN C 13 ASN C 438 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.219244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.177798 restraints weight = 11397.437| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.02 r_work: 0.3538 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13088 Z= 0.151 Angle : 0.590 8.229 17868 Z= 0.306 Chirality : 0.040 0.132 1992 Planarity : 0.005 0.050 2212 Dihedral : 9.985 58.186 2284 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.32 % Allowed : 21.04 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1556 helix: 1.24 (0.16), residues: 1060 sheet: -2.77 (0.63), residues: 48 loop : 1.00 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 311 TYR 0.014 0.001 TYR B 48 PHE 0.014 0.002 PHE D 384 TRP 0.029 0.002 TRP D 411 HIS 0.003 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (13072) covalent geometry : angle 0.58922 / 0.31 (17856) hydrogen bonds : bond 0.05653 / 3.90 ( 836) hydrogen bonds : angle 4.48701 / 3.22 ( 2376) metal coordination : bond 0.00646 / 0.41 ( 16) metal coordination : angle 1.59709 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.356 Fit side-chains REVERT: A 8 GLU cc_start: 0.6776 (tp30) cc_final: 0.6314 (tp30) REVERT: A 89 GLU cc_start: 0.7663 (tp30) cc_final: 0.6631 (mt-10) REVERT: A 201 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6112 (mp) REVERT: A 406 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: A 458 LYS cc_start: 0.6925 (tttt) cc_final: 0.6694 (ttmt) REVERT: B 89 GLU cc_start: 0.7655 (tp30) cc_final: 0.6626 (mt-10) REVERT: B 201 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6104 (mp) REVERT: D 8 GLU cc_start: 0.6727 (tp30) cc_final: 0.6361 (tp30) REVERT: D 89 GLU cc_start: 0.7630 (tp30) cc_final: 0.6636 (mt-10) REVERT: D 201 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6097 (mp) REVERT: D 217 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.6976 (Cg_endo) REVERT: D 379 SER cc_start: 0.7582 (p) cc_final: 0.7207 (m) REVERT: D 406 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8051 (ptm) REVERT: D 422 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8246 (mt) REVERT: D 458 LYS cc_start: 0.6934 (tttt) cc_final: 0.6731 (ttmt) REVERT: C 89 GLU cc_start: 0.7748 (tp30) cc_final: 0.6726 (mt-10) REVERT: C 201 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6123 (mp) REVERT: C 406 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8044 (ptm) REVERT: C 458 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6759 (ttmt) outliers start: 41 outliers final: 27 residues processed: 162 average time/residue: 0.5384 time to fit residues: 94.9157 Evaluate side-chains 161 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 ASN B 438 ASN D 438 ASN C 438 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.219735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.178575 restraints weight = 11359.508| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.03 r_work: 0.3544 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13088 Z= 0.147 Angle : 0.588 9.062 17868 Z= 0.305 Chirality : 0.040 0.130 1992 Planarity : 0.005 0.049 2212 Dihedral : 9.788 59.967 2284 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.16 % Allowed : 21.52 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1556 helix: 1.25 (0.16), residues: 1060 sheet: -2.67 (0.63), residues: 48 loop : 1.02 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.014 0.001 TYR B 48 PHE 0.013 0.001 PHE C 384 TRP 0.037 0.002 TRP B 411 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (13072) covalent geometry : angle 0.58647 / 0.30 (17856) hydrogen bonds : bond 0.05487 / 3.79 ( 836) hydrogen bonds : angle 4.43051 / 3.18 ( 2376) metal coordination : bond 0.00539 / 0.34 ( 16) metal coordination : angle 1.47487 / 0.84 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.293 Fit side-chains REVERT: A 8 GLU cc_start: 0.6825 (tp30) cc_final: 0.6454 (tp30) REVERT: A 89 GLU cc_start: 0.7646 (tp30) cc_final: 0.6613 (mt-10) REVERT: A 201 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6118 (mp) REVERT: A 406 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8109 (ptm) REVERT: A 458 LYS cc_start: 0.6930 (tttt) cc_final: 0.6728 (ttmt) REVERT: B 89 GLU cc_start: 0.7646 (tp30) cc_final: 0.6613 (mt-10) REVERT: B 201 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6131 (mp) REVERT: B 458 LYS cc_start: 0.6924 (tttt) cc_final: 0.6702 (ttmt) REVERT: D 8 GLU cc_start: 0.6770 (tp30) cc_final: 0.6358 (tp30) REVERT: D 89 GLU cc_start: 0.7596 (tp30) cc_final: 0.6589 (mt-10) REVERT: D 201 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6130 (mp) REVERT: D 379 SER cc_start: 0.7570 (p) cc_final: 0.7196 (m) REVERT: D 406 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8105 (ptm) REVERT: D 422 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8255 (mt) REVERT: D 458 LYS cc_start: 0.6926 (tttt) cc_final: 0.6701 (ttmt) REVERT: C 89 GLU cc_start: 0.7770 (tp30) cc_final: 0.6716 (mt-10) REVERT: C 201 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6142 (mp) REVERT: C 406 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8099 (ptm) REVERT: C 458 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6767 (ttmt) outliers start: 39 outliers final: 27 residues processed: 163 average time/residue: 0.5374 time to fit residues: 95.4024 Evaluate side-chains 165 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 458 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 ASN B 438 ASN D 438 ASN C 438 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.220790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.179495 restraints weight = 11425.747| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.08 r_work: 0.3556 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13088 Z= 0.136 Angle : 0.564 8.949 17868 Z= 0.294 Chirality : 0.039 0.131 1992 Planarity : 0.005 0.049 2212 Dihedral : 9.269 58.459 2284 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.99 % Allowed : 22.09 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1556 helix: 1.35 (0.16), residues: 1060 sheet: -2.63 (0.64), residues: 48 loop : 1.04 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 311 TYR 0.014 0.001 TYR C 48 PHE 0.012 0.001 PHE B 384 TRP 0.036 0.002 TRP A 411 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (13072) covalent geometry : angle 0.56340 / 0.29 (17856) hydrogen bonds : bond 0.05186 / 3.59 ( 836) hydrogen bonds : angle 4.35750 / 3.12 ( 2376) metal coordination : bond 0.00427 / 0.27 ( 16) metal coordination : angle 1.35932 / 0.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5649.79 seconds wall clock time: 96 minutes 31.47 seconds (5791.47 seconds total)