Starting phenix.real_space_refine on Fri Jul 3 06:36:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phl_13419/07_2026/7phl_13419.map" } resolution = 3.2 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= 0.016 sd= 0.102 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 4 8.98 5 Zn 4 6.06 5 P 8 5.49 5 S 64 5.16 5 C 8272 2.51 5 N 2064 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s 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: 12604 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3072 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 81 Unusual residues: {' K': 3, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {' K': 1, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 792 SG CYS A 104 74.670 63.686 78.914 1.00107.92 S ATOM 798 SG CYS A 105 72.228 65.678 80.070 1.00105.62 S ATOM 6767 SG CYS B 83 70.601 63.013 80.849 1.00103.76 S ATOM 3864 SG CYS C 104 46.202 57.222 78.998 1.00107.92 S ATOM 3870 SG CYS C 105 48.649 55.233 80.149 1.00105.62 S ATOM 9839 SG CYS D 83 50.455 57.919 80.857 1.00103.76 S ATOM 3695 SG CYS C 83 63.008 50.358 80.885 1.00103.76 S ATOM 6936 SG CYS B 104 63.643 46.243 78.983 1.00107.92 S ATOM 6942 SG CYS B 105 65.647 48.680 80.131 1.00105.62 S ATOM 623 SG CYS A 83 57.881 70.585 80.826 1.00103.76 S ATOM 10008 SG CYS D 104 57.376 74.699 78.944 1.00107.92 S ATOM 10014 SG CYS D 105 55.379 72.260 80.100 1.00105.62 S Time building chain proxies: 3.12, per 1000 atoms: 0.25 Number of scatterers: 12604 At special positions: 0 Unit cell: (121.8, 121.8, 123.48, 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 4 19.00 S 64 16.00 P 8 15.00 O 2188 8.00 N 2064 7.00 C 8272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 609.7 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 A 104 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 105 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 603 " - pdb=" SG CYS D 83 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " Number of angles added : 12 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 4 sheets defined 73.7% alpha, 3.1% 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 22 through 29 removed outlier: 3.515A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.619A pdb=" N HIS A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.554A pdb=" N PHE A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 4.555A 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: 3.540A pdb=" N ASP A 100 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 102 through 110 removed outlier: 4.524A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.510A 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 185 Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.793A pdb=" N ARG A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 266 removed outlier: 3.667A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.039A 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 295 Proline residue: A 288 - end of helix removed outlier: 3.724A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.853A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 326 removed outlier: 4.082A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.776A pdb=" N ARG A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.708A pdb=" N GLY A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'C' and resid 22 through 29 removed outlier: 3.515A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.618A pdb=" N HIS C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.553A pdb=" N PHE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.555A 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: 3.541A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 102 through 110 removed outlier: 4.524A pdb=" N MET C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.510A 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 185 Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.794A pdb=" N ARG C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 266 removed outlier: 3.667A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 4.039A 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 295 Proline residue: C 288 - end of helix removed outlier: 3.724A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.853A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 320 through 326 removed outlier: 4.082A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.776A pdb=" N ARG C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.708A pdb=" N GLY C 390 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 Processing helix chain 'B' and resid 22 through 29 removed outlier: 3.515A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.618A pdb=" N HIS B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.553A pdb=" N PHE B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 4.555A 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: 3.540A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 102 through 110 removed outlier: 4.524A pdb=" N MET B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.510A 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 185 Processing helix chain 'B' and resid 186 through 211 removed outlier: 3.793A pdb=" N ARG B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.667A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 4.039A 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 295 Proline residue: B 288 - end of helix removed outlier: 3.724A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 removed outlier: 3.853A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 320 through 326 removed outlier: 4.081A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.775A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.708A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (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 22 through 29 removed outlier: 3.515A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU D 29 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.618A pdb=" N HIS D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.553A pdb=" N PHE D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 4.554A 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: 3.540A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 102 through 110 removed outlier: 4.525A pdb=" N MET D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.510A 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 185 Processing helix chain 'D' and resid 186 through 211 removed outlier: 3.793A pdb=" N ARG D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 3.667A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 4.040A 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 295 Proline residue: D 288 - end of helix removed outlier: 3.725A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 removed outlier: 3.852A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 320 through 326 removed outlier: 4.082A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.776A pdb=" N ARG D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.707A pdb=" N GLY D 390 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 4.010A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 21 removed outlier: 4.010A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 21 removed outlier: 4.010A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 21 removed outlier: 4.009A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2220 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: 1.84 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1928 1.31 - 1.43: 3780 1.43 - 1.56: 7129 1.56 - 1.69: 19 1.69 - 1.81: 96 Bond restraints: 12952 Sorted by residual: bond pdb=" C21 PCF C 602 " pdb=" O21 PCF C 602 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C21 PCF B 603 " pdb=" O21 PCF B 603 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C21 PCF A 602 " pdb=" O21 PCF A 602 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C21 PCF D 603 " pdb=" O21 PCF D 603 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C31 PCF D 602 " pdb=" O31 PCF D 602 " ideal model delta sigma weight residual 1.329 1.424 -0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 12947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 17353 3.11 - 6.22: 223 6.22 - 9.32: 40 9.32 - 12.43: 4 12.43 - 15.54: 8 Bond angle restraints: 17628 Sorted by residual: angle pdb=" O12 PCF B 603 " pdb=" P PCF B 603 " pdb=" O14 PCF B 603 " ideal model delta sigma weight residual 123.69 108.15 15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O12 PCF D 603 " pdb=" P PCF D 603 " pdb=" O14 PCF D 603 " ideal model delta sigma weight residual 123.69 108.15 15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O12 PCF A 602 " pdb=" P PCF A 602 " pdb=" O14 PCF A 602 " ideal model delta sigma weight residual 123.69 108.17 15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O12 PCF C 602 " pdb=" P PCF C 602 " pdb=" O14 PCF C 602 " ideal model delta sigma weight residual 123.69 108.18 15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" O12 PCF B 602 " pdb=" P PCF B 602 " pdb=" O14 PCF B 602 " ideal model delta sigma weight residual 123.69 109.54 14.15 3.00e+00 1.11e-01 2.22e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.98: 7332 31.98 - 63.97: 276 63.97 - 95.95: 20 95.95 - 127.93: 0 127.93 - 159.92: 4 Dihedral angle restraints: 7632 sinusoidal: 3064 harmonic: 4568 Sorted by residual: dihedral pdb=" O21 PCF D 602 " pdb=" C2 PCF D 602 " pdb=" C3 PCF D 602 " pdb=" O31 PCF D 602 " ideal model delta sinusoidal sigma weight residual 59.47 -100.45 159.92 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O21 PCF C 601 " pdb=" C2 PCF C 601 " pdb=" C3 PCF C 601 " pdb=" O31 PCF C 601 " ideal model delta sinusoidal sigma weight residual 59.47 -100.36 159.83 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O21 PCF A 601 " pdb=" C2 PCF A 601 " pdb=" C3 PCF A 601 " pdb=" O31 PCF A 601 " ideal model delta sinusoidal sigma weight residual 59.47 -100.33 159.80 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1198 0.039 - 0.077: 566 0.077 - 0.116: 132 0.116 - 0.154: 44 0.154 - 0.193: 4 Chirality restraints: 1944 Sorted by residual: chirality pdb=" C2 PCF A 602 " pdb=" C1 PCF A 602 " pdb=" C3 PCF A 602 " pdb=" O21 PCF A 602 " both_signs ideal model delta sigma weight residual False -2.60 -2.40 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" C2 PCF C 602 " pdb=" C1 PCF C 602 " pdb=" C3 PCF C 602 " pdb=" O21 PCF C 602 " both_signs ideal model delta sigma weight residual False -2.60 -2.40 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C2 PCF D 603 " pdb=" C1 PCF D 603 " pdb=" C3 PCF D 603 " pdb=" O21 PCF D 603 " both_signs ideal model delta sigma weight residual False -2.60 -2.40 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1941 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 84 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO C 85 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 84 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 85 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 84 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO D 85 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.030 5.00e-02 4.00e+02 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.96: 6165 2.96 - 3.51: 14755 3.51 - 4.05: 21345 4.05 - 4.60: 33494 4.60 - 5.14: 45470 Nonbonded interactions: 121229 Sorted by model distance: nonbonded pdb=" NH1 ARG C 33 " pdb=" O PHE C 93 " model vdw 2.418 3.120 nonbonded pdb=" NH1 ARG D 33 " pdb=" O PHE D 93 " model vdw 2.419 3.120 nonbonded pdb=" NH1 ARG A 33 " pdb=" O PHE A 93 " model vdw 2.419 3.120 nonbonded pdb=" NH1 ARG B 33 " pdb=" O PHE B 93 " model vdw 2.419 3.120 nonbonded pdb=" NH1 ARG B 263 " pdb=" OD1 ASN B 279 " model vdw 2.424 3.120 ... (remaining 121224 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 or resid 602)) selection = (chain 'B' and (resid 7 through 463 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) selection = (chain 'C' and (resid 7 through 463 or resid 602)) selection = (chain 'D' and (resid 7 through 463 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) } 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: 2.560 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.080 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.010 0.314 12968 Z= 0.428 Angle : 1.136 33.665 17640 Z= 0.456 Chirality : 0.047 0.193 1944 Planarity : 0.006 0.055 2204 Dihedral : 15.992 159.917 4672 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.96 % Allowed : 4.81 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1532 helix: -0.31 (0.15), residues: 960 sheet: -0.26 (0.72), residues: 40 loop : -1.18 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 263 TYR 0.019 0.002 TYR A 109 PHE 0.015 0.002 PHE A 207 TRP 0.010 0.002 TRP B 411 HIS 0.009 0.002 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.37 (12952) covalent geometry : angle 0.91903 / 0.42 (17628) hydrogen bonds : bond 0.11502 / 7.59 ( 756) hydrogen bonds : angle 5.84185 / 4.25 ( 2220) metal coordination : bond 0.16639 / 9.39 ( 16) metal coordination : angle 25.61680 / 14.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.474 Fit side-chains REVERT: A 36 TRP cc_start: 0.6584 (m-10) cc_final: 0.6299 (m-10) REVERT: A 54 GLU cc_start: 0.7785 (pt0) cc_final: 0.7580 (pt0) REVERT: A 107 MET cc_start: 0.8011 (mmp) cc_final: 0.6309 (mpp) REVERT: A 177 TRP cc_start: 0.5229 (t-100) cc_final: 0.5023 (t-100) REVERT: A 213 GLU cc_start: 0.7149 (tt0) cc_final: 0.6792 (tp30) REVERT: A 242 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 263 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.4746 (mtp-110) REVERT: A 406 MET cc_start: 0.8414 (ptp) cc_final: 0.7951 (ptp) REVERT: A 449 LYS cc_start: 0.6875 (mttt) cc_final: 0.6667 (mttp) REVERT: C 48 TYR cc_start: 0.8143 (t80) cc_final: 0.7566 (t80) REVERT: C 81 ASP cc_start: 0.7308 (p0) cc_final: 0.7073 (p0) REVERT: C 213 GLU cc_start: 0.7183 (tt0) cc_final: 0.6903 (tp30) REVERT: C 242 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6988 (mt-10) REVERT: C 406 MET cc_start: 0.8467 (ptp) cc_final: 0.8224 (ptp) REVERT: C 449 LYS cc_start: 0.6793 (mttt) cc_final: 0.6561 (mttp) REVERT: B 36 TRP cc_start: 0.6676 (m-10) cc_final: 0.6413 (m-10) REVERT: B 107 MET cc_start: 0.7953 (mmp) cc_final: 0.6481 (mpp) REVERT: B 213 GLU cc_start: 0.7100 (tt0) cc_final: 0.6782 (tp30) REVERT: B 244 PHE cc_start: 0.5383 (m-80) cc_final: 0.5058 (m-80) REVERT: B 247 TYR cc_start: 0.6270 (m-80) cc_final: 0.5743 (m-10) REVERT: D 36 TRP cc_start: 0.6606 (m-10) cc_final: 0.6253 (m-10) REVERT: D 107 MET cc_start: 0.7921 (mmp) cc_final: 0.6410 (mpp) REVERT: D 213 GLU cc_start: 0.7204 (tt0) cc_final: 0.6908 (tp30) REVERT: D 242 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6993 (mt-10) REVERT: D 263 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.4953 (mtp-110) REVERT: D 290 TYR cc_start: 0.4431 (OUTLIER) cc_final: 0.4143 (m-80) REVERT: D 449 LYS cc_start: 0.6820 (mttt) cc_final: 0.6564 (mttp) outliers start: 12 outliers final: 0 residues processed: 204 average time/residue: 0.1149 time to fit residues: 33.1154 Evaluate side-chains 172 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 290 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN C 111 GLN C 279 ASN B 111 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.216558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.200361 restraints weight = 13083.759| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 0.86 r_work: 0.4080 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12968 Z= 0.159 Angle : 0.567 9.223 17640 Z= 0.277 Chirality : 0.041 0.226 1944 Planarity : 0.005 0.048 2204 Dihedral : 12.348 135.758 2034 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.36 % Allowed : 7.85 % Favored : 90.79 % 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: 0.96 (0.21), residues: 1532 helix: 1.21 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -0.18 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.010 0.001 TYR A 290 PHE 0.019 0.001 PHE A 199 TRP 0.014 0.001 TRP C 177 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (12952) covalent geometry : angle 0.53349 / 0.27 (17628) hydrogen bonds : bond 0.05429 / 3.59 ( 756) hydrogen bonds : angle 4.52123 / 3.28 ( 2220) metal coordination : bond 0.01561 / 0.96 ( 16) metal coordination : angle 7.32531 / 4.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8612 (t80) cc_final: 0.8385 (t80) REVERT: A 67 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 107 MET cc_start: 0.8055 (mmp) cc_final: 0.7736 (mpp) REVERT: C 67 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7839 (mp) REVERT: C 107 MET cc_start: 0.8009 (mmp) cc_final: 0.7770 (mpp) REVERT: B 48 TYR cc_start: 0.8556 (t80) cc_final: 0.8304 (t80) REVERT: B 67 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7826 (mp) REVERT: D 67 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7870 (mp) outliers start: 17 outliers final: 7 residues processed: 180 average time/residue: 0.1034 time to fit residues: 27.8993 Evaluate side-chains 156 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 110 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.216305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.199277 restraints weight = 13143.811| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 0.92 r_work: 0.4087 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12968 Z= 0.155 Angle : 0.550 8.731 17640 Z= 0.267 Chirality : 0.042 0.274 1944 Planarity : 0.005 0.046 2204 Dihedral : 11.467 129.935 2024 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.08 % Allowed : 9.70 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1532 helix: 1.46 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -0.18 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.024 0.001 TYR C 48 PHE 0.020 0.001 PHE C 289 TRP 0.019 0.001 TRP C 177 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (12952) covalent geometry : angle 0.51852 / 0.26 (17628) hydrogen bonds : bond 0.05362 / 3.55 ( 756) hydrogen bonds : angle 4.39379 / 3.19 ( 2220) metal coordination : bond 0.01273 / 0.79 ( 16) metal coordination : angle 7.01237 / 3.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7771 (t0) cc_final: 0.7397 (t0) REVERT: A 67 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 213 GLU cc_start: 0.7301 (tp30) cc_final: 0.7054 (tp30) REVERT: C 48 TYR cc_start: 0.8586 (t80) cc_final: 0.8317 (t80) REVERT: C 53 ASP cc_start: 0.7833 (t0) cc_final: 0.7617 (t0) REVERT: C 67 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7903 (mp) REVERT: B 67 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7913 (mp) REVERT: D 67 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7904 (mp) outliers start: 26 outliers final: 14 residues processed: 167 average time/residue: 0.1008 time to fit residues: 25.6282 Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.212792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190996 restraints weight = 12961.220| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 0.98 r_work: 0.3985 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12968 Z= 0.225 Angle : 0.610 12.222 17640 Z= 0.297 Chirality : 0.044 0.312 1944 Planarity : 0.005 0.051 2204 Dihedral : 11.429 132.905 2024 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 11.94 % Favored : 86.06 % 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: 1.13 (0.21), residues: 1532 helix: 1.34 (0.17), residues: 968 sheet: None (None), residues: 0 loop : -0.18 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.020 0.002 TYR C 48 PHE 0.020 0.002 PHE B 289 TRP 0.016 0.001 TRP C 177 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (12952) covalent geometry : angle 0.56690 / 0.29 (17628) hydrogen bonds : bond 0.06220 / 4.10 ( 756) hydrogen bonds : angle 4.61844 / 3.35 ( 2220) metal coordination : bond 0.01789 / 1.10 ( 16) metal coordination : angle 8.65375 / 4.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.458 Fit side-chains REVERT: A 67 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 213 GLU cc_start: 0.7397 (tp30) cc_final: 0.7176 (tp30) REVERT: C 53 ASP cc_start: 0.7886 (t0) cc_final: 0.7680 (t0) REVERT: C 67 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 53 ASP cc_start: 0.7870 (t0) cc_final: 0.7642 (t0) REVERT: B 67 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.7983 (mp) REVERT: D 67 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.7969 (mp) outliers start: 25 outliers final: 16 residues processed: 155 average time/residue: 0.0931 time to fit residues: 22.2335 Evaluate side-chains 140 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN C 437 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.215616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.198999 restraints weight = 13078.975| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 0.88 r_work: 0.4043 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12968 Z= 0.162 Angle : 0.543 9.390 17640 Z= 0.266 Chirality : 0.041 0.268 1944 Planarity : 0.005 0.047 2204 Dihedral : 11.068 127.860 2024 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.68 % Allowed : 13.38 % Favored : 84.94 % 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: 1.34 (0.21), residues: 1532 helix: 1.47 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -0.04 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.030 0.001 TYR C 48 PHE 0.012 0.001 PHE D 289 TRP 0.020 0.001 TRP D 177 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (12952) covalent geometry : angle 0.51129 / 0.26 (17628) hydrogen bonds : bond 0.05286 / 3.49 ( 756) hydrogen bonds : angle 4.41831 / 3.22 ( 2220) metal coordination : bond 0.01339 / 0.83 ( 16) metal coordination : angle 7.07765 / 3.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8712 (t80) cc_final: 0.8250 (t80) REVERT: A 53 ASP cc_start: 0.7752 (t0) cc_final: 0.7434 (t0) REVERT: A 67 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7899 (mp) REVERT: C 67 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7890 (mp) REVERT: B 48 TYR cc_start: 0.8696 (t80) cc_final: 0.8264 (t80) REVERT: B 53 ASP cc_start: 0.7806 (t0) cc_final: 0.7534 (t0) REVERT: B 67 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7945 (mp) REVERT: D 67 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7932 (mp) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.0910 time to fit residues: 20.9343 Evaluate side-chains 143 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 136 optimal weight: 0.0870 chunk 42 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.211605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.188727 restraints weight = 12950.188| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.03 r_work: 0.3950 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12968 Z= 0.257 Angle : 0.629 12.091 17640 Z= 0.308 Chirality : 0.045 0.294 1944 Planarity : 0.006 0.054 2204 Dihedral : 11.438 133.296 2024 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.56 % Allowed : 12.42 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.21), residues: 1532 helix: 1.24 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -0.31 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 320 TYR 0.031 0.002 TYR C 48 PHE 0.014 0.002 PHE B 315 TRP 0.017 0.002 TRP A 177 HIS 0.007 0.002 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 (12952) covalent geometry : angle 0.58628 / 0.30 (17628) hydrogen bonds : bond 0.06509 / 4.29 ( 756) hydrogen bonds : angle 4.71132 / 3.42 ( 2220) metal coordination : bond 0.01921 / 1.18 ( 16) metal coordination : angle 8.77210 / 4.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7891 (t0) cc_final: 0.7689 (t0) REVERT: A 67 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.7998 (mp) REVERT: C 53 ASP cc_start: 0.7899 (t0) cc_final: 0.7615 (t0) REVERT: C 67 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 48 TYR cc_start: 0.8711 (t80) cc_final: 0.8474 (t80) REVERT: B 53 ASP cc_start: 0.7926 (t0) cc_final: 0.7681 (t0) REVERT: B 67 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.7978 (mp) REVERT: D 67 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.7959 (mp) REVERT: D 458 LYS cc_start: 0.7119 (mttp) cc_final: 0.6892 (mttp) outliers start: 32 outliers final: 20 residues processed: 150 average time/residue: 0.0912 time to fit residues: 21.0769 Evaluate side-chains 143 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 139 optimal weight: 0.0970 chunk 110 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.218097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195515 restraints weight = 12988.877| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.05 r_work: 0.4001 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12968 Z= 0.119 Angle : 0.494 8.551 17640 Z= 0.244 Chirality : 0.039 0.229 1944 Planarity : 0.005 0.045 2204 Dihedral : 10.778 122.704 2024 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.44 % Allowed : 13.94 % Favored : 84.62 % 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: 1.49 (0.22), residues: 1532 helix: 1.60 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -0.01 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.030 0.001 TYR C 48 PHE 0.011 0.001 PHE D 289 TRP 0.019 0.001 TRP A 177 HIS 0.002 0.000 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (12952) covalent geometry : angle 0.47254 / 0.24 (17628) hydrogen bonds : bond 0.04535 / 2.99 ( 756) hydrogen bonds : angle 4.22131 / 3.09 ( 2220) metal coordination : bond 0.00896 / 0.57 ( 16) metal coordination : angle 5.49658 / 3.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7891 (mp) REVERT: C 67 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 48 TYR cc_start: 0.8617 (t80) cc_final: 0.8368 (t80) REVERT: B 53 ASP cc_start: 0.7989 (t0) cc_final: 0.7666 (t0) REVERT: B 67 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 210 GLU cc_start: 0.7333 (tt0) cc_final: 0.7131 (tt0) REVERT: D 67 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7826 (mp) outliers start: 18 outliers final: 11 residues processed: 157 average time/residue: 0.0969 time to fit residues: 23.4569 Evaluate side-chains 150 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 23 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.216735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.193613 restraints weight = 12875.173| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 1.06 r_work: 0.4000 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12968 Z= 0.133 Angle : 0.512 8.982 17640 Z= 0.252 Chirality : 0.040 0.252 1944 Planarity : 0.005 0.044 2204 Dihedral : 10.691 122.568 2024 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.68 % Allowed : 14.42 % Favored : 83.89 % 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: 1.69 (0.22), residues: 1532 helix: 1.80 (0.17), residues: 948 sheet: None (None), residues: 0 loop : 0.07 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 320 TYR 0.029 0.001 TYR C 48 PHE 0.020 0.001 PHE D 93 TRP 0.020 0.001 TRP A 177 HIS 0.004 0.001 HIS D 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12952) covalent geometry : angle 0.48817 / 0.25 (17628) hydrogen bonds : bond 0.04810 / 3.16 ( 756) hydrogen bonds : angle 4.20783 / 3.07 ( 2220) metal coordination : bond 0.00968 / 0.61 ( 16) metal coordination : angle 5.89314 / 3.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7907 (mp) REVERT: C 67 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7891 (mp) REVERT: B 53 ASP cc_start: 0.7989 (t0) cc_final: 0.7675 (t0) REVERT: B 67 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.7922 (mp) REVERT: D 67 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7880 (mp) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.1030 time to fit residues: 23.4755 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 108 optimal weight: 0.2980 chunk 147 optimal weight: 0.0060 chunk 110 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.218408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.200545 restraints weight = 13067.795| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 0.89 r_work: 0.4076 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12968 Z= 0.118 Angle : 0.497 8.477 17640 Z= 0.247 Chirality : 0.039 0.237 1944 Planarity : 0.005 0.044 2204 Dihedral : 10.530 120.353 2024 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.52 % Allowed : 14.82 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.22), residues: 1532 helix: 1.94 (0.17), residues: 948 sheet: -0.15 (0.74), residues: 40 loop : 0.24 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.023 0.001 TYR B 48 PHE 0.012 0.001 PHE A 289 TRP 0.017 0.001 TRP A 177 HIS 0.002 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (12952) covalent geometry : angle 0.47859 / 0.24 (17628) hydrogen bonds : bond 0.04464 / 2.94 ( 756) hydrogen bonds : angle 4.11494 / 3.01 ( 2220) metal coordination : bond 0.00837 / 0.53 ( 16) metal coordination : angle 5.18739 / 2.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7860 (mp) REVERT: C 67 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7840 (mp) REVERT: B 67 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7867 (mp) REVERT: D 67 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7826 (mp) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.0955 time to fit residues: 21.2735 Evaluate side-chains 144 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 HIS D 43 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.216160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.194836 restraints weight = 13009.352| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 0.98 r_work: 0.4025 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12968 Z= 0.152 Angle : 0.528 8.554 17640 Z= 0.261 Chirality : 0.041 0.272 1944 Planarity : 0.005 0.044 2204 Dihedral : 10.715 123.402 2024 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.28 % Allowed : 14.82 % Favored : 83.89 % 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: 1.79 (0.21), residues: 1532 helix: 1.82 (0.17), residues: 956 sheet: -0.27 (0.73), residues: 40 loop : 0.26 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 320 TYR 0.021 0.001 TYR B 48 PHE 0.013 0.001 PHE A 289 TRP 0.014 0.001 TRP A 177 HIS 0.003 0.001 HIS C 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12952) covalent geometry : angle 0.50277 / 0.26 (17628) hydrogen bonds : bond 0.05051 / 3.32 ( 756) hydrogen bonds : angle 4.24576 / 3.10 ( 2220) metal coordination : bond 0.01080 / 0.67 ( 16) metal coordination : angle 6.24242 / 3.50 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.7989 (mp) REVERT: C 67 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.7953 (mp) REVERT: B 67 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.7941 (mp) REVERT: D 67 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7919 (mp) outliers start: 16 outliers final: 11 residues processed: 144 average time/residue: 0.1006 time to fit residues: 21.9905 Evaluate side-chains 146 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS C 43 HIS D 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.218387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.197984 restraints weight = 12985.463| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.02 r_work: 0.4004 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12968 Z= 0.122 Angle : 0.503 8.613 17640 Z= 0.250 Chirality : 0.039 0.239 1944 Planarity : 0.005 0.044 2204 Dihedral : 10.545 121.100 2024 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.36 % Allowed : 14.74 % Favored : 83.89 % 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: 1.96 (0.22), residues: 1532 helix: 2.01 (0.17), residues: 948 sheet: 0.05 (0.78), residues: 40 loop : 0.21 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.022 0.001 TYR B 48 PHE 0.013 0.001 PHE A 289 TRP 0.015 0.001 TRP A 177 HIS 0.002 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (12952) covalent geometry : angle 0.48321 / 0.25 (17628) hydrogen bonds : bond 0.04486 / 2.95 ( 756) hydrogen bonds : angle 4.11275 / 3.01 ( 2220) metal coordination : bond 0.00884 / 0.56 ( 16) metal coordination : angle 5.33128 / 3.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2977.81 seconds wall clock time: 51 minutes 43.24 seconds (3103.24 seconds total)