Starting phenix.real_space_refine on Fri Jul 3 06:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qud_18660/07_2026/8qud_18660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qud_18660/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qud_18660/07_2026/8qud_18660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qud_18660/07_2026/8qud_18660.map" model { file = "/net/cci-nas-00/data/ceres_data/8qud_18660/07_2026/8qud_18660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qud_18660/07_2026/8qud_18660.cif" } 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-dev-6108/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, 108 Ad-hoc single atom residues: {' K': 3} Unusual residues: {' ZN': 1, 'PCF': 1, 'WY0': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 3 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, 108 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' ZN': 1, 'PCF': 1, 'WY0': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 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, 108 Ad-hoc single atom residues: {' K': 2} Unusual residues: {' ZN': 1, 'PCF': 1, 'WY0': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 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: 3.44, per 1000 atoms: 0.27 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: 1.15 Conformation dependent library (CDL) restraints added in 674.8 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: 0.31 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: 2.11 Time building geometry restraints manager: 1.47 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.530 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- 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 : 0.427 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: 0.7044 time to fit residues: 113.0554 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 : 0.501 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.218498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.176196 restraints weight = 11321.899| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.07 r_work: 0.3518 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13088 Z= 0.208 Angle : 0.641 6.397 17868 Z= 0.336 Chirality : 0.043 0.184 1992 Planarity : 0.006 0.054 2212 Dihedral : 11.213 59.914 2286 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.64 % Allowed : 18.69 % 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: 1.46 (0.22), residues: 1556 helix: 1.22 (0.16), residues: 1056 sheet: -3.69 (0.63), residues: 48 loop : 1.25 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.009 0.002 TYR A 407 PHE 0.016 0.002 PHE D 384 TRP 0.011 0.002 TRP D 392 HIS 0.007 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (13072) covalent geometry : angle 0.63841 / 0.34 (17856) hydrogen bonds : bond 0.06801 / 4.67 ( 836) hydrogen bonds : angle 4.76295 / 3.43 ( 2376) metal coordination : bond 0.01195 / 0.75 ( 16) metal coordination : angle 2.20429 / 1.21 ( 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 182 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.482 Fit side-chains REVERT: A 311 ARG cc_start: 0.5075 (tpt90) cc_final: 0.4873 (tpt90) REVERT: D 311 ARG cc_start: 0.5022 (tpt90) cc_final: 0.4803 (tpt90) REVERT: C 89 GLU cc_start: 0.7763 (tp30) cc_final: 0.6784 (mt-10) REVERT: C 441 MET cc_start: 0.8230 (mtt) cc_final: 0.8005 (mtt) REVERT: C 458 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6713 (ttmt) outliers start: 45 outliers final: 12 residues processed: 167 average time/residue: 0.5667 time to fit residues: 102.4772 Evaluate side-chains 149 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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: 10.0000 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: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.214393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.170905 restraints weight = 11340.811| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.30 r_work: 0.3457 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13088 Z= 0.297 Angle : 0.739 6.757 17868 Z= 0.390 Chirality : 0.049 0.186 1992 Planarity : 0.007 0.056 2212 Dihedral : 11.466 57.765 2284 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.74 % Allowed : 16.75 % Favored : 77.51 % 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: 0.91 (0.22), residues: 1556 helix: 0.85 (0.16), residues: 1048 sheet: -3.68 (0.66), residues: 48 loop : 0.87 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 72 TYR 0.012 0.003 TYR D 407 PHE 0.019 0.003 PHE B 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 0.00685 / 0.30 (13072) covalent geometry : angle 0.73534 / 0.39 (17856) hydrogen bonds : bond 0.07924 / 5.43 ( 836) hydrogen bonds : angle 5.07560 / 3.64 ( 2376) metal coordination : bond 0.01015 / 0.63 ( 16) metal coordination : angle 2.80245 / 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 203 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 132 time to evaluate : 0.502 Fit side-chains REVERT: A 201 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6130 (mp) REVERT: B 201 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6113 (mp) REVERT: D 89 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: D 201 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6120 (mp) REVERT: C 201 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6159 (mp) outliers start: 71 outliers final: 30 residues processed: 181 average time/residue: 0.6002 time to fit residues: 118.2779 Evaluate side-chains 162 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 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 450 GLN 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: 0.8980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 GLN B 450 GLN D 450 GLN C 216 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 = 0.4344 r_free = 0.4344 target = 0.220193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.178256 restraints weight = 11498.113| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.07 r_work: 0.3561 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1720 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= 0.144 Angle : 0.562 5.716 17868 Z= 0.292 Chirality : 0.040 0.128 1992 Planarity : 0.005 0.050 2212 Dihedral : 10.680 58.823 2284 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.91 % Allowed : 19.42 % 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: 1.41 (0.22), residues: 1556 helix: 1.23 (0.16), residues: 1052 sheet: -3.29 (0.66), residues: 48 loop : 1.03 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.009 0.001 TYR B 403 PHE 0.013 0.001 PHE B 199 TRP 0.009 0.002 TRP B 94 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (13072) covalent geometry : angle 0.56133 / 0.29 (17856) hydrogen bonds : bond 0.05488 / 3.80 ( 836) hydrogen bonds : angle 4.58916 / 3.30 ( 2376) metal coordination : bond 0.00517 / 0.33 ( 16) metal coordination : angle 1.39343 / 0.79 ( 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 169 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.469 Fit side-chains REVERT: A 89 GLU cc_start: 0.7636 (tp30) cc_final: 0.6616 (mt-10) REVERT: A 201 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6104 (mp) REVERT: A 406 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8166 (ptm) REVERT: B 89 GLU cc_start: 0.7684 (tp30) cc_final: 0.6711 (mt-10) REVERT: B 201 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6108 (mp) REVERT: D 89 GLU cc_start: 0.7631 (tp30) cc_final: 0.6639 (mt-10) REVERT: D 201 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6090 (mp) REVERT: D 406 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8163 (ptm) REVERT: C 89 GLU cc_start: 0.7680 (tp30) cc_final: 0.6698 (mt-10) REVERT: C 201 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6116 (mp) REVERT: C 406 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8155 (ptm) REVERT: C 458 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6687 (ttmt) outliers start: 36 outliers final: 19 residues processed: 151 average time/residue: 0.6357 time to fit residues: 103.7824 Evaluate side-chains 161 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 251 VAL 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 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 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 406 MET 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 251 VAL 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 458 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 ASN B 438 ASN D 438 ASN C 438 ASN C 450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.216171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.174351 restraints weight = 11327.334| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.12 r_work: 0.3482 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2017 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= 0.230 Angle : 0.662 6.308 17868 Z= 0.348 Chirality : 0.045 0.142 1992 Planarity : 0.006 0.054 2212 Dihedral : 10.827 59.804 2284 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.69 % Allowed : 18.04 % Favored : 77.27 % 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: 1.14 (0.22), residues: 1556 helix: 1.05 (0.16), residues: 1048 sheet: -3.24 (0.66), residues: 48 loop : 0.86 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.010 0.002 TYR B 407 PHE 0.018 0.002 PHE C 64 TRP 0.013 0.002 TRP B 94 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (13072) covalent geometry : angle 0.65931 / 0.35 (17856) hydrogen bonds : bond 0.07011 / 4.82 ( 836) hydrogen bonds : angle 4.84142 / 3.47 ( 2376) metal coordination : bond 0.00870 / 0.54 ( 16) metal coordination : angle 2.27947 / 1.27 ( 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 183 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 125 time to evaluate : 0.456 Fit side-chains REVERT: A 8 GLU cc_start: 0.6690 (tp30) cc_final: 0.6338 (tp30) REVERT: A 201 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6168 (mp) REVERT: B 201 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6171 (mp) REVERT: B 406 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8079 (ptm) REVERT: D 8 GLU cc_start: 0.6692 (tp30) cc_final: 0.6339 (tp30) REVERT: D 201 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6163 (mp) REVERT: C 201 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6162 (mp) REVERT: C 458 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6731 (ttmt) outliers start: 58 outliers final: 28 residues processed: 167 average time/residue: 0.5736 time to fit residues: 104.2004 Evaluate side-chains 153 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 444 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 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 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 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: 0.9980 chunk 135 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 216 ASN C 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.219446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174730 restraints weight = 11380.458| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.06 r_work: 0.3645 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1948 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= 0.151 Angle : 0.578 6.533 17868 Z= 0.300 Chirality : 0.040 0.128 1992 Planarity : 0.005 0.050 2212 Dihedral : 10.305 59.704 2284 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.96 % Allowed : 19.58 % 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: 1.41 (0.22), residues: 1556 helix: 1.24 (0.16), residues: 1052 sheet: -2.98 (0.66), residues: 48 loop : 0.98 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 311 TYR 0.010 0.001 TYR D 48 PHE 0.014 0.002 PHE C 384 TRP 0.012 0.002 TRP C 411 HIS 0.003 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (13072) covalent geometry : angle 0.57712 / 0.30 (17856) hydrogen bonds : bond 0.05660 / 3.91 ( 836) hydrogen bonds : angle 4.55843 / 3.27 ( 2376) metal coordination : bond 0.00536 / 0.34 ( 16) metal coordination : angle 1.49829 / 0.85 ( 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 177 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.497 Fit side-chains REVERT: A 8 GLU cc_start: 0.6814 (tp30) cc_final: 0.6429 (tp30) REVERT: A 89 GLU cc_start: 0.7447 (tp30) cc_final: 0.6570 (mt-10) REVERT: A 201 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6019 (mp) REVERT: A 406 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8027 (ptm) REVERT: A 458 LYS cc_start: 0.6969 (tttt) cc_final: 0.6740 (ttmt) REVERT: B 89 GLU cc_start: 0.7455 (tp30) cc_final: 0.6617 (mt-10) REVERT: B 201 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6028 (mp) REVERT: B 406 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8100 (ptm) REVERT: B 458 LYS cc_start: 0.6968 (tttt) cc_final: 0.6749 (ttmt) REVERT: D 89 GLU cc_start: 0.7509 (tp30) cc_final: 0.6603 (mt-10) REVERT: D 201 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6008 (mp) REVERT: D 406 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8022 (ptm) REVERT: D 458 LYS cc_start: 0.6961 (tttt) cc_final: 0.6742 (ttmt) REVERT: C 89 GLU cc_start: 0.7448 (tp30) cc_final: 0.6624 (mt-10) REVERT: C 201 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6034 (mp) REVERT: C 406 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8016 (ptm) REVERT: C 458 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6773 (ttmt) outliers start: 49 outliers final: 26 residues processed: 163 average time/residue: 0.5788 time to fit residues: 102.6742 Evaluate side-chains 161 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 B residue 24 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 240 GLU 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 D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 176 ILE 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 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 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: 0.8980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.214261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172268 restraints weight = 11269.177| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.13 r_work: 0.3456 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2283 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 : 0.740 7.126 17868 Z= 0.391 Chirality : 0.049 0.155 1992 Planarity : 0.006 0.056 2212 Dihedral : 10.926 57.485 2284 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.61 % Allowed : 19.74 % 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: 0.87 (0.21), residues: 1556 helix: 0.81 (0.16), residues: 1052 sheet: -3.22 (0.67), residues: 48 loop : 0.82 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 311 TYR 0.014 0.003 TYR B 48 PHE 0.019 0.003 PHE C 64 TRP 0.016 0.003 TRP A 411 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (13072) covalent geometry : angle 0.73789 / 0.39 (17856) hydrogen bonds : bond 0.07816 / 5.36 ( 836) hydrogen bonds : angle 4.96982 / 3.56 ( 2376) metal coordination : bond 0.00708 / 0.43 ( 16) metal coordination : angle 2.45240 / 1.38 ( 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 184 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 0.491 Fit side-chains REVERT: A 8 GLU cc_start: 0.6802 (tp30) cc_final: 0.6407 (tp30) REVERT: A 201 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6140 (mp) REVERT: B 201 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6181 (mp) REVERT: B 406 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8051 (ptm) REVERT: D 201 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6162 (mp) REVERT: C 201 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6164 (mp) outliers start: 57 outliers final: 37 residues processed: 168 average time/residue: 0.5999 time to fit residues: 109.2950 Evaluate side-chains 163 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 444 SER Chi-restraints excluded: chain B residue 24 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 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 444 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 176 ILE 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 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 240 GLU 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: 6.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.220432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.179397 restraints weight = 11393.546| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.00 r_work: 0.3563 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13088 Z= 0.138 Angle : 0.573 8.285 17868 Z= 0.297 Chirality : 0.039 0.128 1992 Planarity : 0.005 0.050 2212 Dihedral : 10.131 59.311 2284 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.29 % Allowed : 19.90 % Favored : 75.81 % 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: 1.18 (0.16), residues: 1060 sheet: -2.94 (0.66), residues: 48 loop : 1.06 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.011 0.001 TYR B 48 PHE 0.013 0.001 PHE C 384 TRP 0.019 0.002 TRP D 411 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (13072) covalent geometry : angle 0.57250 / 0.30 (17856) hydrogen bonds : bond 0.05313 / 3.68 ( 836) hydrogen bonds : angle 4.48278 / 3.22 ( 2376) metal coordination : bond 0.00388 / 0.25 ( 16) metal coordination : angle 1.35956 / 0.78 ( 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 194 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.469 Fit side-chains REVERT: A 8 GLU cc_start: 0.6811 (tp30) cc_final: 0.6327 (tp30) REVERT: A 89 GLU cc_start: 0.7611 (tp30) cc_final: 0.6569 (mt-10) REVERT: A 201 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6093 (mp) REVERT: A 458 LYS cc_start: 0.6878 (tttt) cc_final: 0.6628 (ttmt) REVERT: B 8 GLU cc_start: 0.6679 (tp30) cc_final: 0.6317 (tp30) REVERT: B 89 GLU cc_start: 0.7717 (tp30) cc_final: 0.6692 (mt-10) REVERT: B 201 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6133 (mp) REVERT: B 458 LYS cc_start: 0.6870 (tttt) cc_final: 0.6612 (ttmt) REVERT: D 8 GLU cc_start: 0.6672 (tp30) cc_final: 0.6314 (tp30) REVERT: D 89 GLU cc_start: 0.7617 (tp30) cc_final: 0.6588 (mt-10) REVERT: D 201 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6113 (mp) REVERT: D 379 SER cc_start: 0.7568 (p) cc_final: 0.7186 (m) REVERT: D 422 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8217 (mt) REVERT: D 458 LYS cc_start: 0.6880 (tttt) cc_final: 0.6625 (ttmt) REVERT: C 8 GLU cc_start: 0.6695 (tp30) cc_final: 0.6341 (tp30) REVERT: C 89 GLU cc_start: 0.7723 (tp30) cc_final: 0.6698 (mt-10) REVERT: C 201 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6121 (mp) REVERT: C 458 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6688 (ttmt) outliers start: 53 outliers final: 26 residues processed: 175 average time/residue: 0.5898 time to fit residues: 112.4611 Evaluate side-chains 167 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 379 SER Chi-restraints excluded: chain A residue 412 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 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 240 GLU 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 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: 1.9990 chunk 5 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.217053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174626 restraints weight = 11378.618| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.11 r_work: 0.3501 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13088 Z= 0.200 Angle : 0.650 8.060 17868 Z= 0.340 Chirality : 0.043 0.139 1992 Planarity : 0.006 0.052 2212 Dihedral : 10.254 56.380 2284 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.80 % Allowed : 20.47 % Favored : 75.73 % 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: 1.22 (0.22), residues: 1556 helix: 1.05 (0.16), residues: 1060 sheet: -2.87 (0.65), residues: 48 loop : 1.01 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 311 TYR 0.014 0.002 TYR B 48 PHE 0.017 0.002 PHE B 64 TRP 0.029 0.003 TRP D 411 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (13072) covalent geometry : angle 0.64771 / 0.34 (17856) hydrogen bonds : bond 0.06532 / 4.49 ( 836) hydrogen bonds : angle 4.67298 / 3.35 ( 2376) metal coordination : bond 0.00802 / 0.50 ( 16) metal coordination : angle 2.03795 / 1.14 ( 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 175 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.419 Fit side-chains REVERT: A 8 GLU cc_start: 0.6752 (tp30) cc_final: 0.6268 (tp30) REVERT: A 89 GLU cc_start: 0.7655 (tp30) cc_final: 0.6633 (mt-10) REVERT: A 201 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6118 (mp) REVERT: B 8 GLU cc_start: 0.6752 (tp30) cc_final: 0.6405 (tp30) REVERT: B 89 GLU cc_start: 0.7751 (tp30) cc_final: 0.6743 (mt-10) REVERT: B 201 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6162 (mp) REVERT: D 8 GLU cc_start: 0.6716 (tp30) cc_final: 0.6359 (tp30) REVERT: D 89 GLU cc_start: 0.7652 (tp30) cc_final: 0.6631 (mt-10) REVERT: D 201 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6113 (mp) REVERT: D 379 SER cc_start: 0.7612 (p) cc_final: 0.7238 (m) REVERT: D 422 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8249 (mt) REVERT: C 8 GLU cc_start: 0.6736 (tp30) cc_final: 0.6383 (tp30) REVERT: C 89 GLU cc_start: 0.7769 (tp30) cc_final: 0.6754 (mt-10) REVERT: C 201 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6138 (mp) REVERT: C 458 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6736 (ttmt) outliers start: 47 outliers final: 32 residues processed: 164 average time/residue: 0.6318 time to fit residues: 112.6704 Evaluate side-chains 166 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 379 SER 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 261 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 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 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: 6.9990 chunk 117 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.219323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.177098 restraints weight = 11422.120| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.05 r_work: 0.3547 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2142 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= 0.154 Angle : 0.600 8.766 17868 Z= 0.312 Chirality : 0.040 0.135 1992 Planarity : 0.005 0.050 2212 Dihedral : 9.962 59.212 2284 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.24 % Allowed : 21.04 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.22), residues: 1556 helix: 1.14 (0.16), residues: 1060 sheet: -2.69 (0.64), residues: 48 loop : 1.06 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.014 0.002 TYR B 48 PHE 0.014 0.002 PHE A 384 TRP 0.032 0.002 TRP D 411 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13072) covalent geometry : angle 0.59929 / 0.31 (17856) hydrogen bonds : bond 0.05636 / 3.89 ( 836) hydrogen bonds : angle 4.50151 / 3.23 ( 2376) metal coordination : bond 0.00559 / 0.35 ( 16) metal coordination : angle 1.57015 / 0.89 ( 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 170 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.488 Fit side-chains REVERT: A 8 GLU cc_start: 0.6773 (tp30) cc_final: 0.6415 (tp30) REVERT: A 89 GLU cc_start: 0.7622 (tp30) cc_final: 0.6580 (mt-10) REVERT: A 201 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6090 (mp) REVERT: A 422 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 8 GLU cc_start: 0.6749 (tp30) cc_final: 0.6384 (tp30) REVERT: B 89 GLU cc_start: 0.7673 (tp30) cc_final: 0.6692 (mt-10) REVERT: B 201 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6112 (mp) REVERT: B 422 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8233 (mt) REVERT: D 8 GLU cc_start: 0.6754 (tp30) cc_final: 0.6384 (tp30) REVERT: D 89 GLU cc_start: 0.7615 (tp30) cc_final: 0.6592 (mt-10) REVERT: D 201 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6094 (mp) REVERT: D 379 SER cc_start: 0.7590 (p) cc_final: 0.7214 (m) REVERT: D 422 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8241 (mt) REVERT: C 8 GLU cc_start: 0.6798 (tp30) cc_final: 0.6429 (tp30) REVERT: C 89 GLU cc_start: 0.7688 (tp30) cc_final: 0.6706 (mt-10) REVERT: C 201 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.6103 (mp) REVERT: C 422 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8240 (mt) REVERT: C 458 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6723 (ttmt) outliers start: 40 outliers final: 27 residues processed: 164 average time/residue: 0.6085 time to fit residues: 108.8419 Evaluate side-chains 164 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 323 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 422 LEU 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 422 LEU 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 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 267 CYS Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 422 LEU 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: 0.9990 chunk 52 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.218198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.175237 restraints weight = 11412.299| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.12 r_work: 0.3533 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13088 Z= 0.172 Angle : 0.616 8.715 17868 Z= 0.323 Chirality : 0.041 0.136 1992 Planarity : 0.005 0.051 2212 Dihedral : 9.946 59.908 2284 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.91 % Allowed : 21.12 % Favored : 75.97 % 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: 1.28 (0.22), residues: 1556 helix: 1.09 (0.16), residues: 1060 sheet: -2.73 (0.64), residues: 48 loop : 1.03 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 311 TYR 0.016 0.002 TYR B 48 PHE 0.015 0.002 PHE B 384 TRP 0.037 0.003 TRP A 411 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (13072) covalent geometry : angle 0.61481 / 0.32 (17856) hydrogen bonds : bond 0.06003 / 4.14 ( 836) hydrogen bonds : angle 4.56276 / 3.27 ( 2376) metal coordination : bond 0.00675 / 0.43 ( 16) metal coordination : angle 1.73880 / 0.98 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5705.68 seconds wall clock time: 97 minutes 41.84 seconds (5861.84 seconds total)