Starting phenix.real_space_refine on Thu Aug 6 01:19:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8quc_18659/08_2026/8quc_18659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8quc_18659/08_2026/8quc_18659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8quc_18659/08_2026/8quc_18659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8quc_18659/08_2026/8quc_18659.map" model { file = "/net/cci-nas-00/data/ceres_data/8quc_18659/08_2026/8quc_18659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8quc_18659/08_2026/8quc_18659.cif" } resolution = 2.9 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= 0.004 sd= 0.042 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 5 8.98 5 Zn 4 6.06 5 P 4 5.49 5 S 68 5.16 5 C 8412 2.51 5 N 2088 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12829 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3090 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3090 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3090 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3090 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 201 Unusual residues: {' K': 5, ' ZN': 1, 'PCF': 3, 'WY9': 1, 'Y01': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' ZN': 1, 'PCF': 1, 'WY9': 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: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' ZN': 1, 'WY9': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' ZN': 1, 'WY9': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 792 SG CYS A 104 71.338 52.714 43.010 1.00 33.55 S ATOM 798 SG CYS A 105 68.298 50.864 41.587 1.00 28.95 S ATOM 3713 SG CYS B 83 68.151 54.327 41.516 1.00 49.11 S ATOM 3882 SG CYS B 104 63.634 71.322 43.010 1.00 33.55 S ATOM 3888 SG CYS B 105 65.485 68.283 41.586 1.00 28.95 S ATOM 9893 SG CYS C 83 62.048 68.175 41.530 1.00 49.11 S ATOM 623 SG CYS A 83 54.341 48.202 41.522 1.00 49.11 S ATOM 6972 SG CYS D 104 52.703 44.983 43.020 1.00 33.55 S ATOM 6978 SG CYS D 105 50.850 48.019 41.595 1.00 28.95 S ATOM 6803 SG CYS D 83 48.176 61.974 41.516 1.00 49.11 S ATOM 10062 SG CYS C 104 45.050 63.656 42.996 1.00 33.55 S ATOM 10068 SG CYS C 105 48.091 65.508 41.577 1.00 28.95 S Time building chain proxies: 3.54, per 1000 atoms: 0.28 Number of scatterers: 12829 At special positions: 0 Unit cell: (117.171, 117.171, 122.157, 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 5 19.00 S 68 16.00 P 4 15.00 O 2248 8.00 N 2088 7.00 C 8412 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: 1.25 Conformation dependent library (CDL) restraints added in 630.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 105 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 104 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 603 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 105 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 104 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 602 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 104 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 602 " - 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 4 sheets defined 74.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 removed outlier: 4.475A pdb=" N LEU A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) 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: 4.132A 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: 3.715A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 4.379A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.634A pdb=" N SER A 186 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 211 removed outlier: 4.180A pdb=" N TYR A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 266 removed outlier: 3.895A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 276 through 298 Proline residue: A 288 - end of helix removed outlier: 3.873A pdb=" N GLY A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 298 " --> pdb=" O GLY A 294 " (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 326 removed outlier: 3.904A 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 380 removed outlier: 3.828A pdb=" N SER A 379 " --> pdb=" O PRO A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.683A pdb=" N GLY A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 3.675A 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 29 removed outlier: 4.475A pdb=" N LEU B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) 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: 4.131A 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: 3.714A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 removed outlier: 4.379A pdb=" N MET B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.634A pdb=" N SER B 186 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 211 removed outlier: 4.180A pdb=" N TYR B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.896A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 276 through 298 Proline residue: B 288 - end of helix removed outlier: 3.873A pdb=" N GLY B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 298 " --> pdb=" O GLY B 294 " (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 326 removed outlier: 3.904A 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 380 removed outlier: 3.829A pdb=" N SER B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.683A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) removed outlier: 3.675A 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 29 removed outlier: 4.474A pdb=" N LEU D 29 " --> pdb=" O THR D 25 " (cutoff:3.500A) 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: 4.133A 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: 3.715A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 110 removed outlier: 4.379A pdb=" N MET D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR D 108 " --> pdb=" O CYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.635A pdb=" N SER D 186 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 211 removed outlier: 4.180A pdb=" N TYR D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 3.895A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 276 through 298 Proline residue: D 288 - end of helix removed outlier: 3.872A pdb=" N GLY D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU D 298 " --> pdb=" O GLY D 294 " (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 326 removed outlier: 3.903A 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 380 removed outlier: 3.828A pdb=" N SER D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.684A pdb=" N GLY D 390 " --> pdb=" O ASN D 386 " (cutoff:3.500A) removed outlier: 3.676A 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 29 removed outlier: 4.475A pdb=" N LEU C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) 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: 4.132A 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: 3.715A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 removed outlier: 4.379A pdb=" N MET C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR C 108 " --> pdb=" O CYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.634A pdb=" N SER C 186 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 211 removed outlier: 4.180A pdb=" N TYR C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 266 removed outlier: 3.896A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 276 through 298 Proline residue: C 288 - end of helix removed outlier: 3.873A pdb=" N GLY C 297 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 298 " --> pdb=" O GLY C 294 " (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 326 removed outlier: 3.903A 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 380 removed outlier: 3.828A pdb=" N SER C 379 " --> pdb=" O PRO C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.683A pdb=" N GLY C 390 " --> pdb=" O ASN C 386 " (cutoff:3.500A) removed outlier: 3.675A 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 removed outlier: 3.883A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.883A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.882A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.882A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2304 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: 2.51 Time building geometry restraints manager: 1.62 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: 1956 1.31 - 1.44: 3848 1.44 - 1.56: 7236 1.56 - 1.69: 16 1.69 - 1.81: 104 Bond restraints: 13160 Sorted by residual: bond pdb=" C21 PCF A 605 " pdb=" O21 PCF A 605 " ideal model delta sigma weight residual 1.334 1.429 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C21 PCF B 602 " pdb=" O21 PCF B 602 " ideal model delta sigma weight residual 1.334 1.429 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C21 PCF A 602 " pdb=" O21 PCF A 602 " ideal model delta sigma weight residual 1.334 1.429 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C21 PCF A 606 " pdb=" O21 PCF A 606 " ideal model delta sigma weight residual 1.334 1.428 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C31 PCF A 605 " pdb=" O31 PCF A 605 " ideal model delta sigma weight residual 1.329 1.420 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 13155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 17704 2.95 - 5.89: 217 5.89 - 8.84: 15 8.84 - 11.79: 8 11.79 - 14.74: 4 Bond angle restraints: 17948 Sorted by residual: angle pdb=" O12 PCF A 605 " pdb=" P PCF A 605 " pdb=" O14 PCF A 605 " ideal model delta sigma weight residual 123.69 108.95 14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" O12 PCF B 602 " pdb=" P PCF B 602 " pdb=" O14 PCF B 602 " ideal model delta sigma weight residual 123.69 108.96 14.73 3.00e+00 1.11e-01 2.41e+01 angle pdb=" O12 PCF A 602 " pdb=" P PCF A 602 " pdb=" O14 PCF A 602 " ideal model delta sigma weight residual 123.69 108.97 14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" O12 PCF A 606 " pdb=" P PCF A 606 " pdb=" O14 PCF A 606 " ideal model delta sigma weight residual 123.69 108.99 14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" C32 PCF B 602 " pdb=" C31 PCF B 602 " pdb=" O31 PCF B 602 " ideal model delta sigma weight residual 111.48 121.15 -9.67 3.00e+00 1.11e-01 1.04e+01 ... (remaining 17943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 6795 16.88 - 33.76: 757 33.76 - 50.65: 258 50.65 - 67.53: 66 67.53 - 84.41: 16 Dihedral angle restraints: 7892 sinusoidal: 3284 harmonic: 4608 Sorted by residual: dihedral pdb=" CA THR D 427 " pdb=" C THR D 427 " pdb=" N ILE D 428 " pdb=" CA ILE D 428 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR B 427 " pdb=" C THR B 427 " pdb=" N ILE B 428 " pdb=" CA ILE B 428 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR A 427 " pdb=" C THR A 427 " pdb=" N ILE A 428 " pdb=" CA ILE A 428 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1605 0.045 - 0.090: 311 0.090 - 0.135: 68 0.135 - 0.180: 0 0.180 - 0.225: 4 Chirality restraints: 1988 Sorted by residual: chirality pdb=" C3 WY9 B 601 " pdb=" C18 WY9 B 601 " pdb=" C2 WY9 B 601 " pdb=" N1 WY9 B 601 " both_signs ideal model delta sigma weight residual False -2.58 -2.80 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3 WY9 A 601 " pdb=" C18 WY9 A 601 " pdb=" C2 WY9 A 601 " pdb=" N1 WY9 A 601 " both_signs ideal model delta sigma weight residual False -2.58 -2.80 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3 WY9 C 601 " pdb=" C18 WY9 C 601 " pdb=" C2 WY9 C 601 " pdb=" N1 WY9 C 601 " both_signs ideal model delta sigma weight residual False -2.58 -2.80 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1985 not shown) Planarity restraints: 2232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 WY9 A 601 " -0.044 2.00e-02 2.50e+03 1.65e-01 5.47e+02 pdb=" C3 WY9 A 601 " 0.132 2.00e-02 2.50e+03 pdb=" C4 WY9 A 601 " -0.038 2.00e-02 2.50e+03 pdb=" C5 WY9 A 601 " 0.235 2.00e-02 2.50e+03 pdb=" N1 WY9 A 601 " 0.149 2.00e-02 2.50e+03 pdb=" N2 WY9 A 601 " 0.052 2.00e-02 2.50e+03 pdb=" O1 WY9 A 601 " -0.248 2.00e-02 2.50e+03 pdb=" O4 WY9 A 601 " -0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 WY9 B 601 " -0.044 2.00e-02 2.50e+03 1.65e-01 5.46e+02 pdb=" C3 WY9 B 601 " 0.132 2.00e-02 2.50e+03 pdb=" C4 WY9 B 601 " -0.038 2.00e-02 2.50e+03 pdb=" C5 WY9 B 601 " 0.235 2.00e-02 2.50e+03 pdb=" N1 WY9 B 601 " 0.149 2.00e-02 2.50e+03 pdb=" N2 WY9 B 601 " 0.052 2.00e-02 2.50e+03 pdb=" O1 WY9 B 601 " -0.248 2.00e-02 2.50e+03 pdb=" O4 WY9 B 601 " -0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 WY9 D 601 " 0.044 2.00e-02 2.50e+03 1.65e-01 5.46e+02 pdb=" C3 WY9 D 601 " -0.132 2.00e-02 2.50e+03 pdb=" C4 WY9 D 601 " 0.037 2.00e-02 2.50e+03 pdb=" C5 WY9 D 601 " -0.235 2.00e-02 2.50e+03 pdb=" N1 WY9 D 601 " -0.148 2.00e-02 2.50e+03 pdb=" N2 WY9 D 601 " -0.052 2.00e-02 2.50e+03 pdb=" O1 WY9 D 601 " 0.248 2.00e-02 2.50e+03 pdb=" O4 WY9 D 601 " 0.238 2.00e-02 2.50e+03 ... (remaining 2229 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 1379 2.75 - 3.34: 15192 3.34 - 3.94: 24733 3.94 - 4.54: 35952 4.54 - 5.14: 51964 Nonbonded interactions: 129220 Sorted by model distance: nonbonded pdb=" OE2 GLU D 249 " pdb=" O HOH D 701 " model vdw 2.147 3.040 nonbonded pdb=" OE2 GLU A 249 " pdb=" O HOH A 701 " model vdw 2.148 3.040 nonbonded pdb=" OE2 GLU B 249 " pdb=" O HOH B 701 " model vdw 2.148 3.040 nonbonded pdb=" OE2 GLU C 249 " pdb=" O HOH C 701 " model vdw 2.148 3.040 nonbonded pdb=" NH1 ARG A 33 " pdb=" O PHE A 93 " model vdw 2.279 3.120 ... (remaining 129215 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 601) selection = (chain 'B' and resid 7 through 601) selection = (chain 'C' and resid 7 through 601) selection = (chain 'D' and resid 7 through 601) } 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: 2.530 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.150 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 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 0.095 13176 Z= 0.263 Angle : 0.773 14.736 17960 Z= 0.354 Chirality : 0.038 0.225 1988 Planarity : 0.009 0.165 2232 Dihedral : 16.805 84.410 4908 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.51 % Allowed : 18.87 % Favored : 79.62 % 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: 0.90 (0.21), residues: 1556 helix: 1.25 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -0.43 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 263 TYR 0.012 0.001 TYR D 70 PHE 0.009 0.001 PHE B 93 TRP 0.010 0.001 TRP B 255 HIS 0.005 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.26 (13160) covalent geometry : angle 0.74505 / 0.35 (17948) hydrogen bonds : bond 0.10254 / 6.75 ( 796) hydrogen bonds : angle 4.78684 / 3.47 ( 2304) metal coordination : bond 0.01983 / 1.08 ( 16) metal coordination : angle 8.02536 / 4.15 ( 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 188 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: D 8 GLU cc_start: 0.7853 (tp30) cc_final: 0.7174 (tt0) REVERT: C 263 ARG cc_start: 0.7015 (mtp-110) cc_final: 0.6733 (mtp85) outliers start: 19 outliers final: 8 residues processed: 188 average time/residue: 0.3777 time to fit residues: 79.4378 Evaluate side-chains 170 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 286 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A 437 ASN A 438 ASN B 276 ASN B 327 HIS B 437 ASN B 438 ASN D 276 ASN D 327 HIS D 437 ASN D 438 ASN C 276 ASN C 327 HIS C 437 ASN C 438 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.188253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143444 restraints weight = 12493.650| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.69 r_work: 0.3135 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13176 Z= 0.145 Angle : 0.570 14.378 17960 Z= 0.272 Chirality : 0.040 0.129 1988 Planarity : 0.005 0.054 2232 Dihedral : 10.493 67.744 2256 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.26 % Allowed : 17.68 % Favored : 79.06 % 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: 1.52 (0.21), residues: 1556 helix: 1.59 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 0.13 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.010 0.001 TYR B 365 PHE 0.013 0.001 PHE D 180 TRP 0.010 0.001 TRP A 255 HIS 0.006 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (13160) covalent geometry : angle 0.52592 / 0.27 (17948) hydrogen bonds : bond 0.05385 / 3.63 ( 796) hydrogen bonds : angle 4.25735 / 3.10 ( 2304) metal coordination : bond 0.01251 / 0.76 ( 16) metal coordination : angle 8.56293 / 4.38 ( 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 216 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.454 Fit side-chains REVERT: B 8 GLU cc_start: 0.7448 (tp30) cc_final: 0.6639 (tt0) REVERT: D 8 GLU cc_start: 0.7463 (tp30) cc_final: 0.6761 (tt0) REVERT: D 346 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8141 (tp) outliers start: 41 outliers final: 12 residues processed: 204 average time/residue: 0.3800 time to fit residues: 86.5971 Evaluate side-chains 174 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 437 ASN A 438 ASN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 437 ASN B 438 ASN D 276 ASN D 437 ASN D 438 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 437 ASN C 438 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.184358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138852 restraints weight = 12492.473| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.94 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13176 Z= 0.188 Angle : 0.616 15.688 17960 Z= 0.293 Chirality : 0.042 0.140 1988 Planarity : 0.005 0.056 2232 Dihedral : 10.390 72.817 2252 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.62 % Allowed : 17.68 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1556 helix: 1.45 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 0.25 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 263 TYR 0.013 0.002 TYR D 365 PHE 0.016 0.002 PHE C 180 TRP 0.012 0.002 TRP A 255 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (13160) covalent geometry : angle 0.56354 / 0.29 (17948) hydrogen bonds : bond 0.06244 / 4.21 ( 796) hydrogen bonds : angle 4.45141 / 3.24 ( 2304) metal coordination : bond 0.01459 / 0.91 ( 16) metal coordination : angle 9.64580 / 4.94 ( 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 234 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.453 Fit side-chains REVERT: A 8 GLU cc_start: 0.7395 (tp30) cc_final: 0.6786 (tt0) REVERT: A 277 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8029 (p) REVERT: B 8 GLU cc_start: 0.7391 (tp30) cc_final: 0.6782 (tt0) REVERT: D 8 GLU cc_start: 0.7341 (tp30) cc_final: 0.6734 (tt0) REVERT: D 277 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8027 (p) REVERT: D 346 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8021 (tp) REVERT: C 8 GLU cc_start: 0.7484 (tp30) cc_final: 0.6861 (tt0) REVERT: C 277 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.7999 (p) outliers start: 58 outliers final: 20 residues processed: 216 average time/residue: 0.4330 time to fit residues: 103.6480 Evaluate side-chains 183 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain D residue 180 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A 327 HIS A 437 ASN B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 437 ASN D 276 ASN D 327 HIS D 437 ASN C 276 ASN C 327 HIS C 437 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.187523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145097 restraints weight = 12515.597| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.61 r_work: 0.3101 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13176 Z= 0.127 Angle : 0.531 11.723 17960 Z= 0.255 Chirality : 0.039 0.128 1988 Planarity : 0.005 0.051 2232 Dihedral : 10.173 67.504 2252 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.50 % Allowed : 19.98 % Favored : 76.51 % 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: 1.83 (0.21), residues: 1556 helix: 1.74 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 0.44 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 263 TYR 0.011 0.001 TYR D 48 PHE 0.011 0.001 PHE D 180 TRP 0.011 0.001 TRP B 255 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13160) covalent geometry : angle 0.49535 / 0.25 (17948) hydrogen bonds : bond 0.04998 / 3.36 ( 796) hydrogen bonds : angle 4.19162 / 3.05 ( 2304) metal coordination : bond 0.01171 / 0.73 ( 16) metal coordination : angle 7.39240 / 3.80 ( 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 234 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.451 Fit side-chains REVERT: A 8 GLU cc_start: 0.7311 (tp30) cc_final: 0.6554 (tt0) REVERT: B 8 GLU cc_start: 0.7308 (tp30) cc_final: 0.6605 (tt0) REVERT: D 8 GLU cc_start: 0.7323 (tp30) cc_final: 0.6566 (tt0) REVERT: C 8 GLU cc_start: 0.7423 (tp30) cc_final: 0.6685 (tt0) outliers start: 44 outliers final: 16 residues processed: 216 average time/residue: 0.4649 time to fit residues: 111.3044 Evaluate side-chains 193 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 81 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 437 ASN A 438 ASN B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 437 ASN B 438 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS D 437 ASN D 438 ASN C 276 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 437 ASN C 438 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.187060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140096 restraints weight = 12539.373| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.41 r_work: 0.3195 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13176 Z= 0.145 Angle : 0.546 11.353 17960 Z= 0.263 Chirality : 0.040 0.132 1988 Planarity : 0.005 0.051 2232 Dihedral : 10.157 68.807 2252 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.66 % Allowed : 19.82 % Favored : 76.51 % 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: 1.93 (0.21), residues: 1556 helix: 1.80 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 0.54 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 263 TYR 0.010 0.001 TYR B 365 PHE 0.011 0.001 PHE C 180 TRP 0.009 0.001 TRP D 255 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13160) covalent geometry : angle 0.51162 / 0.26 (17948) hydrogen bonds : bond 0.05362 / 3.61 ( 796) hydrogen bonds : angle 4.18019 / 3.05 ( 2304) metal coordination : bond 0.01224 / 0.76 ( 16) metal coordination : angle 7.40168 / 3.82 ( 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 239 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.319 Fit side-chains REVERT: A 8 GLU cc_start: 0.7228 (tp30) cc_final: 0.6585 (tt0) REVERT: B 8 GLU cc_start: 0.7211 (tp30) cc_final: 0.6558 (tt0) REVERT: B 292 GLU cc_start: 0.7002 (tt0) cc_final: 0.6650 (tt0) REVERT: D 8 GLU cc_start: 0.7239 (tp30) cc_final: 0.6626 (tt0) REVERT: D 314 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7686 (mtp180) REVERT: C 8 GLU cc_start: 0.7273 (tp30) cc_final: 0.6649 (tt0) outliers start: 46 outliers final: 11 residues processed: 226 average time/residue: 0.4733 time to fit residues: 118.4979 Evaluate side-chains 193 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 437 ASN A 438 ASN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 437 ASN B 438 ASN D 276 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS D 437 ASN D 438 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 437 ASN C 438 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.187299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130577 restraints weight = 12521.026| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.04 r_work: 0.3213 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13176 Z= 0.135 Angle : 0.531 10.283 17960 Z= 0.258 Chirality : 0.039 0.127 1988 Planarity : 0.005 0.050 2232 Dihedral : 10.093 67.551 2248 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.50 % Allowed : 20.46 % Favored : 76.04 % 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: 2.00 (0.22), residues: 1556 helix: 1.85 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 0.58 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 263 TYR 0.012 0.001 TYR B 48 PHE 0.013 0.001 PHE B 180 TRP 0.009 0.001 TRP B 255 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (13160) covalent geometry : angle 0.50101 / 0.25 (17948) hydrogen bonds : bond 0.05112 / 3.44 ( 796) hydrogen bonds : angle 4.14556 / 3.02 ( 2304) metal coordination : bond 0.01107 / 0.69 ( 16) metal coordination : angle 6.85266 / 3.55 ( 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 229 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.487 Fit side-chains REVERT: A 8 GLU cc_start: 0.7188 (tp30) cc_final: 0.6432 (tt0) REVERT: B 8 GLU cc_start: 0.7143 (tp30) cc_final: 0.6403 (tt0) REVERT: B 292 GLU cc_start: 0.6875 (tt0) cc_final: 0.6545 (tt0) REVERT: D 8 GLU cc_start: 0.7225 (tp30) cc_final: 0.6422 (tt0) REVERT: D 314 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7595 (mtp180) REVERT: C 8 GLU cc_start: 0.7171 (tp30) cc_final: 0.6420 (tt0) outliers start: 44 outliers final: 15 residues processed: 212 average time/residue: 0.5303 time to fit residues: 123.9358 Evaluate side-chains 191 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 133 optimal weight: 0.0270 chunk 132 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 437 ASN A 438 ASN B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 437 ASN B 438 ASN D 276 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS D 437 ASN D 438 ASN C 216 ASN C 276 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 437 ASN C 438 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.190271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132972 restraints weight = 12557.907| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.02 r_work: 0.3256 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13176 Z= 0.112 Angle : 0.492 8.691 17960 Z= 0.242 Chirality : 0.038 0.130 1988 Planarity : 0.004 0.047 2232 Dihedral : 9.896 63.302 2244 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.63 % Allowed : 20.78 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.22), residues: 1556 helix: 2.02 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 0.71 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.015 0.001 TYR C 48 PHE 0.016 0.001 PHE D 180 TRP 0.008 0.001 TRP D 255 HIS 0.002 0.000 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (13160) covalent geometry : angle 0.46679 / 0.24 (17948) hydrogen bonds : bond 0.04499 / 3.02 ( 796) hydrogen bonds : angle 3.98986 / 2.90 ( 2304) metal coordination : bond 0.01021 / 0.63 ( 16) metal coordination : angle 6.04321 / 3.14 ( 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 220 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.459 Fit side-chains REVERT: A 8 GLU cc_start: 0.7100 (tp30) cc_final: 0.6443 (tt0) REVERT: B 8 GLU cc_start: 0.7044 (tp30) cc_final: 0.6444 (tt0) REVERT: B 292 GLU cc_start: 0.6956 (tt0) cc_final: 0.6591 (tt0) REVERT: D 8 GLU cc_start: 0.7115 (tp30) cc_final: 0.6446 (tt0) REVERT: C 8 GLU cc_start: 0.7121 (tp30) cc_final: 0.6447 (tt0) outliers start: 33 outliers final: 14 residues processed: 209 average time/residue: 0.4760 time to fit residues: 110.1498 Evaluate side-chains 188 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 406 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 438 ASN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 438 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 438 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 276 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 438 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.183139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141498 restraints weight = 12513.185| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.39 r_work: 0.3213 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13176 Z= 0.250 Angle : 0.649 12.042 17960 Z= 0.317 Chirality : 0.045 0.155 1988 Planarity : 0.005 0.055 2232 Dihedral : 10.559 72.189 2244 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.87 % Allowed : 21.58 % Favored : 75.56 % 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: 1.30 (0.21), residues: 1556 helix: 1.41 (0.16), residues: 992 sheet: -3.20 (0.62), residues: 52 loop : 0.41 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 263 TYR 0.019 0.002 TYR C 48 PHE 0.017 0.002 PHE D 180 TRP 0.010 0.002 TRP D 94 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.25 (13160) covalent geometry : angle 0.61268 / 0.31 (17948) hydrogen bonds : bond 0.06776 / 4.57 ( 796) hydrogen bonds : angle 4.50014 / 3.28 ( 2304) metal coordination : bond 0.01617 / 1.00 ( 16) metal coordination : angle 8.26046 / 4.29 ( 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 197 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7236 (tp30) cc_final: 0.6696 (tt0) REVERT: A 279 ASN cc_start: 0.8551 (m110) cc_final: 0.8281 (m110) REVERT: B 8 GLU cc_start: 0.7246 (tp30) cc_final: 0.6676 (tt0) REVERT: D 279 ASN cc_start: 0.8572 (m110) cc_final: 0.8316 (m110) REVERT: C 8 GLU cc_start: 0.7364 (tp30) cc_final: 0.6722 (tt0) outliers start: 36 outliers final: 17 residues processed: 182 average time/residue: 0.5695 time to fit residues: 113.4940 Evaluate side-chains 177 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 147 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 130 optimal weight: 0.0070 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 152 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN D 216 ASN D 276 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS D 437 ASN C 216 ASN C 276 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 437 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.189624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132441 restraints weight = 12609.264| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.06 r_work: 0.3225 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13176 Z= 0.114 Angle : 0.505 9.009 17960 Z= 0.251 Chirality : 0.038 0.134 1988 Planarity : 0.005 0.049 2232 Dihedral : 10.247 62.729 2244 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.51 % Allowed : 22.29 % Favored : 76.19 % 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: 2.06 (0.22), residues: 1556 helix: 1.91 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 0.56 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 263 TYR 0.014 0.001 TYR B 48 PHE 0.017 0.001 PHE D 180 TRP 0.012 0.001 TRP C 255 HIS 0.002 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13160) covalent geometry : angle 0.47877 / 0.25 (17948) hydrogen bonds : bond 0.04619 / 3.10 ( 796) hydrogen bonds : angle 4.12109 / 3.00 ( 2304) metal coordination : bond 0.00980 / 0.61 ( 16) metal coordination : angle 6.22988 / 3.24 ( 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 202 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.458 Fit side-chains REVERT: A 8 GLU cc_start: 0.7004 (tp30) cc_final: 0.6535 (tt0) REVERT: B 8 GLU cc_start: 0.7036 (tp30) cc_final: 0.6576 (tt0) REVERT: B 292 GLU cc_start: 0.6920 (tt0) cc_final: 0.6534 (tt0) REVERT: D 8 GLU cc_start: 0.7032 (tp30) cc_final: 0.6550 (tt0) REVERT: C 8 GLU cc_start: 0.7159 (tp30) cc_final: 0.6520 (tt0) outliers start: 19 outliers final: 12 residues processed: 193 average time/residue: 0.5555 time to fit residues: 117.4064 Evaluate side-chains 190 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN D 216 ASN D 276 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 438 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 276 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128498 restraints weight = 12569.008| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.04 r_work: 0.3214 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13176 Z= 0.149 Angle : 0.544 9.783 17960 Z= 0.269 Chirality : 0.040 0.134 1988 Planarity : 0.005 0.058 2232 Dihedral : 10.273 65.451 2244 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.59 % Allowed : 22.69 % Favored : 75.72 % 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: 1.90 (0.22), residues: 1556 helix: 1.85 (0.16), residues: 972 sheet: -2.98 (0.63), residues: 52 loop : 0.80 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 263 TYR 0.016 0.001 TYR C 48 PHE 0.020 0.001 PHE A 180 TRP 0.009 0.001 TRP D 255 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (13160) covalent geometry : angle 0.51550 / 0.27 (17948) hydrogen bonds : bond 0.05377 / 3.62 ( 796) hydrogen bonds : angle 4.21858 / 3.07 ( 2304) metal coordination : bond 0.01145 / 0.72 ( 16) metal coordination : angle 6.71146 / 3.48 ( 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 198 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.473 Fit side-chains REVERT: A 8 GLU cc_start: 0.7049 (tp30) cc_final: 0.6529 (tt0) REVERT: B 8 GLU cc_start: 0.7029 (tp30) cc_final: 0.6496 (tt0) REVERT: B 292 GLU cc_start: 0.6938 (tt0) cc_final: 0.6575 (tt0) REVERT: D 8 GLU cc_start: 0.7041 (tp30) cc_final: 0.6494 (tt0) REVERT: C 8 GLU cc_start: 0.7160 (tp30) cc_final: 0.6558 (tt0) outliers start: 20 outliers final: 17 residues processed: 188 average time/residue: 0.5615 time to fit residues: 115.8022 Evaluate side-chains 190 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 438 ASN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 438 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN D 276 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 438 ASN C 216 ASN C 276 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 438 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.187754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141930 restraints weight = 12568.349| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.38 r_work: 0.3222 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13176 Z= 0.134 Angle : 0.526 9.452 17960 Z= 0.261 Chirality : 0.040 0.129 1988 Planarity : 0.005 0.061 2232 Dihedral : 10.308 63.795 2244 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.67 % Allowed : 22.37 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.22), residues: 1556 helix: 1.90 (0.16), residues: 972 sheet: -2.87 (0.65), residues: 52 loop : 0.81 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 263 TYR 0.015 0.001 TYR C 48 PHE 0.021 0.001 PHE D 180 TRP 0.010 0.001 TRP D 255 HIS 0.002 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13160) covalent geometry : angle 0.49884 / 0.26 (17948) hydrogen bonds : bond 0.05070 / 3.42 ( 796) hydrogen bonds : angle 4.17278 / 3.04 ( 2304) metal coordination : bond 0.01062 / 0.66 ( 16) metal coordination : angle 6.50314 / 3.38 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4108.97 seconds wall clock time: 70 minutes 45.10 seconds (4245.10 seconds total)