Starting phenix.real_space_refine on Thu Mar 5 16:03:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9i_25758/03_2026/7t9i_25758_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9i_25758/03_2026/7t9i_25758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9i_25758/03_2026/7t9i_25758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9i_25758/03_2026/7t9i_25758.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9i_25758/03_2026/7t9i_25758_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9i_25758/03_2026/7t9i_25758_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 100 5.16 5 C 7620 2.51 5 N 2028 2.21 5 O 2224 1.98 5 H 11557 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1205 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1636 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1893 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 9416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9416 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 568} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3286 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 102 Chain: "Y" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5110 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "Z" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.76, per 1000 atoms: 0.16 Number of scatterers: 23529 At special positions: 0 Unit cell: (103.272, 99.962, 202.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 O 2224 8.00 N 2028 7.00 C 7620 6.00 H 11557 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 87 " distance=2.02 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 85 " distance=2.04 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 31 " distance=2.03 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.03 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 301 " - pdb=" SG CYS R 390 " distance=2.04 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 101 " - " ASN A 78 " " NAG B 201 " - " ASN B 23 " " NAG C 1 " - " ASN A 52 " " NAG R 801 " - " ASN R 99 " " NAG R 802 " - " ASN R 77 " " NAG R 803 " - " ASN R 198 " " NAG R 804 " - " ASN R 177 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 960.5 milliseconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 32.2% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.625A pdb=" N SER B 48 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.688A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.507A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 172 through 176 removed outlier: 3.791A pdb=" N LEU R 175 " --> pdb=" O PHE R 172 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS R 176 " --> pdb=" O GLN R 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 176' Processing helix chain 'R' and resid 218 through 222 removed outlier: 4.464A pdb=" N PHE R 221 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.622A pdb=" N LYS R 287 " --> pdb=" O CYS R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 304 Processing helix chain 'R' and resid 381 through 391 Processing helix chain 'R' and resid 416 through 442 removed outlier: 4.834A pdb=" N TRP R 422 " --> pdb=" O ARG R 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 447 through 477 Processing helix chain 'R' and resid 480 through 491 removed outlier: 3.731A pdb=" N HIS R 484 " --> pdb=" O GLU R 480 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE R 486 " --> pdb=" O TYR R 482 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 525 removed outlier: 4.163A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 528 through 532 Processing helix chain 'R' and resid 534 through 559 removed outlier: 3.572A pdb=" N ALA R 538 " --> pdb=" O ARG R 534 " (cutoff:3.500A) Proline residue: R 556 - end of helix removed outlier: 3.511A pdb=" N GLY R 559 " --> pdb=" O LEU R 555 " (cutoff:3.500A) Processing helix chain 'R' and resid 576 through 609 Processing helix chain 'R' and resid 620 through 649 removed outlier: 3.902A pdb=" N LEU R 629 " --> pdb=" O ARG R 625 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 666 removed outlier: 3.776A pdb=" N LYS R 660 " --> pdb=" O VAL R 656 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 668 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 682 through 697 Processing helix chain 'X' and resid 15 through 39 Processing helix chain 'X' and resid 52 through 59 Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.521A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 279 Processing helix chain 'X' and resid 293 through 304 removed outlier: 3.528A pdb=" N GLY X 304 " --> pdb=" O LYS X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 Processing helix chain 'X' and resid 331 through 352 removed outlier: 3.947A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER X 352 " --> pdb=" O ILE X 348 " (cutoff:3.500A) Processing helix chain 'X' and resid 370 through 391 Processing helix chain 'Y' and resid 4 through 25 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Z' and resid 8 through 24 removed outlier: 3.541A pdb=" N ASN Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 45 Processing helix chain 'Z' and resid 46 through 48 No H-bonds generated for 'chain 'Z' and resid 46 through 48' Processing helix chain 'Z' and resid 55 through 59 removed outlier: 3.670A pdb=" N GLU Z 58 " --> pdb=" O PRO Z 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 4.160A pdb=" N CYS A 32 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS B 31 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N THR B 25 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 67 removed outlier: 6.129A pdb=" N ALA A 81 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR A 65 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N HIS A 79 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 67 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU A 77 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 63 removed outlier: 6.759A pdb=" N SER B 82 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE B 57 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 80 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR B 59 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR B 61 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 76 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 63 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 74 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.535A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.549A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 30 through 33 removed outlier: 3.648A pdb=" N ARG R 38 " --> pdb=" O HIS R 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR R 56 " --> pdb=" O PHE R 37 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU R 57 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N SER R 84 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU R 59 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR R 111 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR R 136 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN R 110 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU R 131 " --> pdb=" O GLU R 157 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR R 159 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE R 133 " --> pdb=" O THR R 159 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU R 180 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA R 204 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP R 203 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA R 275 " --> pdb=" O THR R 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.320A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'R' and resid 166 through 167 removed outlier: 3.573A pdb=" N ILE R 167 " --> pdb=" O SER R 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 210 through 214 removed outlier: 10.205A pdb=" N ALA X 243 " --> pdb=" O THR X 40 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ARG X 42 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE X 245 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU X 44 " --> pdb=" O ILE X 245 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL X 247 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU X 46 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP X 249 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Y' and resid 46 through 51 removed outlier: 6.644A pdb=" N ILE Y 338 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR Y 50 " --> pdb=" O LEU Y 336 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU Y 336 " --> pdb=" O THR Y 50 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS Y 317 " --> pdb=" O GLY Y 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Y 79 " --> pdb=" O ILE Y 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 100 through 105 removed outlier: 7.027A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY Y 116 " --> pdb=" O ILE Y 120 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE Y 120 " --> pdb=" O GLY Y 116 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU Y 139 " --> pdb=" O CYS Y 121 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN Y 125 " --> pdb=" O VAL Y 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL Y 135 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 146 through 151 removed outlier: 3.724A pdb=" N CYS Y 148 " --> pdb=" O SER Y 160 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 187 through 192 removed outlier: 7.047A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA Y 203 " --> pdb=" O SER Y 207 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER Y 207 " --> pdb=" O ALA Y 203 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP Y 212 " --> pdb=" O CYS Y 218 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS Y 218 " --> pdb=" O ASP Y 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 231 through 234 removed outlier: 3.735A pdb=" N ALA Y 231 " --> pdb=" O GLY Y 244 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS Y 250 " --> pdb=" O THR Y 263 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR Y 263 " --> pdb=" O CYS Y 250 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU Y 252 " --> pdb=" O LEU Y 261 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN Y 259 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 273 through 278 removed outlier: 3.597A pdb=" N SER Y 275 " --> pdb=" O GLY Y 288 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11523 1.02 - 1.23: 57 1.23 - 1.43: 5136 1.43 - 1.63: 6939 1.63 - 1.83: 132 Bond restraints: 23787 Sorted by residual: bond pdb=" ND2 ASN A 15 " pdb="HD21 ASN A 15 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN X 23 " pdb="HD22 ASN X 23 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN X 23 " pdb="HD21 ASN X 23 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 15 " pdb="HD22 ASN A 15 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN A 52 " pdb="HD21 ASN A 52 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.11e+01 ... (remaining 23782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 41314 1.93 - 3.86: 1252 3.86 - 5.80: 166 5.80 - 7.73: 24 7.73 - 9.66: 10 Bond angle restraints: 42766 Sorted by residual: angle pdb=" C ASN A 15 " pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " ideal model delta sigma weight residual 108.86 99.99 8.87 1.44e+00 4.82e-01 3.79e+01 angle pdb=" N PHE A 74 " pdb=" CA PHE A 74 " pdb=" C PHE A 74 " ideal model delta sigma weight residual 110.41 117.56 -7.15 1.23e+00 6.61e-01 3.38e+01 angle pdb=" CA GLU X 21 " pdb=" C GLU X 21 " pdb=" N ALA X 22 " ideal model delta sigma weight residual 117.07 110.47 6.60 1.14e+00 7.69e-01 3.35e+01 angle pdb=" C PHE A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta sigma weight residual 122.84 130.14 -7.30 1.30e+00 5.92e-01 3.16e+01 angle pdb=" C LYS X 24 " pdb=" N LYS X 25 " pdb=" CA LYS X 25 " ideal model delta sigma weight residual 120.28 127.35 -7.07 1.34e+00 5.57e-01 2.78e+01 ... (remaining 42761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10350 17.84 - 35.68: 825 35.68 - 53.52: 222 53.52 - 71.37: 55 71.37 - 89.21: 27 Dihedral angle restraints: 11479 sinusoidal: 6141 harmonic: 5338 Sorted by residual: dihedral pdb=" CB CYS R 494 " pdb=" SG CYS R 494 " pdb=" SG CYS R 569 " pdb=" CB CYS R 569 " ideal model delta sinusoidal sigma weight residual -86.00 -35.08 -50.92 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS R 301 " pdb=" SG CYS R 301 " pdb=" SG CYS R 390 " pdb=" CB CYS R 390 " ideal model delta sinusoidal sigma weight residual -86.00 -130.41 44.41 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA THR A 86 " pdb=" C THR A 86 " pdb=" N CYS A 87 " pdb=" CA CYS A 87 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 11476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1766 0.091 - 0.182: 159 0.182 - 0.273: 7 0.273 - 0.365: 1 0.365 - 0.456: 1 Chirality restraints: 1934 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.90e+01 chirality pdb=" C1 NAG A 101 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG A 101 " pdb=" O5 NAG A 101 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 52 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1931 not shown) Planarity restraints: 3566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 15 " 0.265 2.00e-02 2.50e+03 4.54e-01 3.09e+03 pdb=" CG ASN A 15 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 15 " -0.258 2.00e-02 2.50e+03 pdb=" ND2 ASN A 15 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 15 " 0.749 2.00e-02 2.50e+03 pdb="HD22 ASN A 15 " -0.734 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN X 23 " 0.292 2.00e-02 2.50e+03 3.04e-01 1.38e+03 pdb=" CG ASN X 23 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN X 23 " -0.261 2.00e-02 2.50e+03 pdb=" ND2 ASN X 23 " -0.005 2.00e-02 2.50e+03 pdb="HD21 ASN X 23 " -0.434 2.00e-02 2.50e+03 pdb="HD22 ASN X 23 " 0.457 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.305 2.00e-02 2.50e+03 2.65e-01 8.81e+02 pdb=" C7 NAG C 1 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.464 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.198 2.00e-02 2.50e+03 ... (remaining 3563 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2688 2.26 - 2.84: 51425 2.84 - 3.43: 59957 3.43 - 4.01: 82640 4.01 - 4.60: 125495 Nonbonded interactions: 322205 Sorted by model distance: nonbonded pdb=" O ALA R 380 " pdb=" HG SER R 383 " model vdw 1.670 2.450 nonbonded pdb=" H LYS R 291 " pdb=" O GLU R 394 " model vdw 1.694 2.450 nonbonded pdb=" HZ1 LYS X 233 " pdb=" OD2 ASP Y 228 " model vdw 1.696 2.450 nonbonded pdb=" O LYS R 250 " pdb=" H THR R 273 " model vdw 1.702 2.450 nonbonded pdb=" O ILE B 36 " pdb=" HZ2 LYS B 39 " model vdw 1.709 2.450 ... (remaining 322200 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 11.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 12254 Z= 0.301 Angle : 0.936 13.338 16668 Z= 0.526 Chirality : 0.052 0.456 1934 Planarity : 0.010 0.265 2096 Dihedral : 12.776 84.578 4482 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.62 % Allowed : 1.01 % Favored : 98.36 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.16 (0.22), residues: 1510 helix: 1.51 (0.25), residues: 428 sheet: -1.14 (0.29), residues: 305 loop : -0.52 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 13 TYR 0.018 0.002 TYR Y 124 PHE 0.039 0.002 PHE Z 61 TRP 0.022 0.002 TRP Y 339 HIS 0.005 0.001 HIS Y 225 Details of bonding type rmsd covalent geometry : bond 0.00531 (12230) covalent geometry : angle 0.91492 (16612) SS BOND : bond 0.00563 ( 16) SS BOND : angle 1.84455 ( 32) hydrogen bonds : bond 0.14151 ( 498) hydrogen bonds : angle 6.94786 ( 1398) link_BETA1-4 : bond 0.00661 ( 1) link_BETA1-4 : angle 4.96460 ( 3) link_NAG-ASN : bond 0.05215 ( 7) link_NAG-ASN : angle 4.99401 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 269 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7561 (m) REVERT: B 9 MET cc_start: 0.6858 (ptp) cc_final: 0.6628 (tpp) REVERT: B 79 VAL cc_start: 0.7531 (t) cc_final: 0.7314 (m) REVERT: B 82 SER cc_start: 0.6713 (t) cc_final: 0.6363 (p) REVERT: R 22 MET cc_start: -0.1957 (tpt) cc_final: -0.2210 (mtp) REVERT: R 61 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6087 (mt-10) REVERT: R 91 GLN cc_start: 0.5635 (mt0) cc_final: 0.4895 (mp10) REVERT: R 116 TYR cc_start: 0.8038 (t80) cc_final: 0.7710 (t80) REVERT: R 434 PHE cc_start: 0.7498 (t80) cc_final: 0.7232 (t80) REVERT: R 510 TYR cc_start: 0.7008 (t80) cc_final: 0.6661 (t80) REVERT: R 572 MET cc_start: 0.5164 (mmm) cc_final: 0.4815 (mtt) REVERT: R 681 PHE cc_start: 0.6230 (m-10) cc_final: 0.6003 (m-80) REVERT: R 683 LYS cc_start: 0.8004 (mmpt) cc_final: 0.7740 (mtmm) REVERT: Y 114 CYS cc_start: 0.7527 (p) cc_final: 0.7258 (p) REVERT: Y 126 LEU cc_start: 0.6777 (tt) cc_final: 0.6470 (mp) REVERT: Y 127 LYS cc_start: 0.5767 (mttm) cc_final: 0.5142 (ptpp) REVERT: Z 26 ASP cc_start: 0.6184 (p0) cc_final: 0.5835 (p0) REVERT: Z 38 MET cc_start: 0.5789 (ptt) cc_final: 0.4881 (pp-130) outliers start: 8 outliers final: 1 residues processed: 271 average time/residue: 0.9740 time to fit residues: 291.3870 Evaluate side-chains 180 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain X residue 352 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 135 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 GLN Y 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.133642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.116216 restraints weight = 84075.978| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.38 r_work: 0.4001 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12254 Z= 0.201 Angle : 0.633 5.667 16668 Z= 0.340 Chirality : 0.043 0.183 1934 Planarity : 0.005 0.058 2096 Dihedral : 6.462 53.854 1833 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.03 % Allowed : 10.38 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.15 (0.21), residues: 1510 helix: 1.76 (0.25), residues: 421 sheet: -1.24 (0.29), residues: 299 loop : -0.61 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 256 TYR 0.015 0.002 TYR B 59 PHE 0.021 0.002 PHE X 212 TRP 0.028 0.003 TRP Y 82 HIS 0.004 0.001 HIS X 362 Details of bonding type rmsd covalent geometry : bond 0.00438 (12230) covalent geometry : angle 0.62658 (16612) SS BOND : bond 0.00608 ( 16) SS BOND : angle 1.17800 ( 32) hydrogen bonds : bond 0.05951 ( 498) hydrogen bonds : angle 5.41401 ( 1398) link_BETA1-4 : bond 0.00031 ( 1) link_BETA1-4 : angle 3.89760 ( 3) link_NAG-ASN : bond 0.00544 ( 7) link_NAG-ASN : angle 1.77170 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 SER cc_start: 0.6695 (t) cc_final: 0.6429 (p) REVERT: R 22 MET cc_start: -0.1728 (tpt) cc_final: -0.2157 (mtp) REVERT: R 394 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: R 414 TYR cc_start: 0.6677 (m-80) cc_final: 0.6266 (m-80) REVERT: R 434 PHE cc_start: 0.8081 (t80) cc_final: 0.7773 (t80) REVERT: R 572 MET cc_start: 0.5345 (mmm) cc_final: 0.5073 (mtt) REVERT: R 681 PHE cc_start: 0.6595 (m-10) cc_final: 0.6154 (m-80) REVERT: Y 105 TYR cc_start: 0.6967 (t80) cc_final: 0.6713 (t80) REVERT: Y 126 LEU cc_start: 0.7098 (tt) cc_final: 0.6787 (mp) REVERT: Y 127 LYS cc_start: 0.5949 (mttm) cc_final: 0.5063 (ptpp) REVERT: Z 26 ASP cc_start: 0.6091 (p0) cc_final: 0.5813 (p0) REVERT: Z 38 MET cc_start: 0.5833 (ptt) cc_final: 0.4915 (pp-130) outliers start: 26 outliers final: 12 residues processed: 199 average time/residue: 0.9155 time to fit residues: 202.7528 Evaluate side-chains 172 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 394 GLU Chi-restraints excluded: chain R residue 591 ILE Chi-restraints excluded: chain R residue 626 MET Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 90 HIS Y 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.130819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.113310 restraints weight = 83547.309| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.35 r_work: 0.3958 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12254 Z= 0.200 Angle : 0.613 6.110 16668 Z= 0.329 Chirality : 0.043 0.169 1934 Planarity : 0.005 0.068 2096 Dihedral : 6.228 57.594 1831 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.80 % Allowed : 14.60 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.37 (0.21), residues: 1510 helix: 1.74 (0.25), residues: 424 sheet: -1.23 (0.29), residues: 302 loop : -0.94 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 13 TYR 0.014 0.002 TYR R 279 PHE 0.019 0.002 PHE X 212 TRP 0.021 0.003 TRP Y 82 HIS 0.005 0.001 HIS X 362 Details of bonding type rmsd covalent geometry : bond 0.00442 (12230) covalent geometry : angle 0.60696 (16612) SS BOND : bond 0.00385 ( 16) SS BOND : angle 1.35905 ( 32) hydrogen bonds : bond 0.05899 ( 498) hydrogen bonds : angle 5.22795 ( 1398) link_BETA1-4 : bond 0.01195 ( 1) link_BETA1-4 : angle 3.21784 ( 3) link_NAG-ASN : bond 0.00398 ( 7) link_NAG-ASN : angle 1.69660 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 SER cc_start: 0.6632 (t) cc_final: 0.6350 (p) REVERT: N 28 THR cc_start: 0.8830 (t) cc_final: 0.8455 (m) REVERT: R 22 MET cc_start: -0.1742 (tpt) cc_final: -0.2103 (mtp) REVERT: R 394 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6657 (pm20) REVERT: R 414 TYR cc_start: 0.6711 (m-80) cc_final: 0.6289 (m-80) REVERT: R 633 ASP cc_start: 0.7395 (t0) cc_final: 0.6887 (m-30) REVERT: X 378 ASP cc_start: 0.6506 (m-30) cc_final: 0.5991 (m-30) REVERT: Y 105 TYR cc_start: 0.6920 (t80) cc_final: 0.6666 (t80) REVERT: Y 126 LEU cc_start: 0.7292 (tt) cc_final: 0.6997 (mp) REVERT: Y 127 LYS cc_start: 0.6005 (mttm) cc_final: 0.5265 (ptpp) REVERT: Z 13 ARG cc_start: 0.6699 (mtm110) cc_final: 0.6279 (ptp-170) REVERT: Z 26 ASP cc_start: 0.5866 (p0) cc_final: 0.5616 (p0) REVERT: Z 38 MET cc_start: 0.5972 (ptt) cc_final: 0.5073 (pp-130) outliers start: 23 outliers final: 15 residues processed: 187 average time/residue: 0.8312 time to fit residues: 173.8664 Evaluate side-chains 175 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 394 GLU Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 626 MET Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Z residue 17 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.129122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.111464 restraints weight = 82899.713| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.35 r_work: 0.3922 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12254 Z= 0.233 Angle : 0.634 5.626 16668 Z= 0.342 Chirality : 0.043 0.166 1934 Planarity : 0.005 0.054 2096 Dihedral : 6.401 56.910 1831 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.73 % Allowed : 15.53 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.57 (0.21), residues: 1510 helix: 1.61 (0.25), residues: 425 sheet: -1.36 (0.29), residues: 301 loop : -1.08 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 231 TYR 0.015 0.002 TYR R 279 PHE 0.021 0.002 PHE X 212 TRP 0.019 0.003 TRP N 47 HIS 0.027 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00520 (12230) covalent geometry : angle 0.62614 (16612) SS BOND : bond 0.00630 ( 16) SS BOND : angle 1.68373 ( 32) hydrogen bonds : bond 0.06094 ( 498) hydrogen bonds : angle 5.21149 ( 1398) link_BETA1-4 : bond 0.00829 ( 1) link_BETA1-4 : angle 3.21601 ( 3) link_NAG-ASN : bond 0.00429 ( 7) link_NAG-ASN : angle 1.75348 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8145 (t) cc_final: 0.7881 (m) REVERT: B 82 SER cc_start: 0.6647 (t) cc_final: 0.6338 (p) REVERT: N 28 THR cc_start: 0.8869 (t) cc_final: 0.8519 (m) REVERT: R 22 MET cc_start: -0.1511 (tpt) cc_final: -0.1972 (mtp) REVERT: R 44 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7484 (pt) REVERT: R 394 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: R 414 TYR cc_start: 0.6727 (m-80) cc_final: 0.6313 (m-80) REVERT: R 633 ASP cc_start: 0.7430 (t0) cc_final: 0.6884 (m-30) REVERT: Y 126 LEU cc_start: 0.7345 (tt) cc_final: 0.7091 (mp) REVERT: Y 127 LYS cc_start: 0.6004 (mttm) cc_final: 0.5337 (ptpp) REVERT: Z 38 MET cc_start: 0.5994 (ptt) cc_final: 0.5125 (pp-130) REVERT: Z 42 GLU cc_start: 0.5515 (pt0) cc_final: 0.5182 (pp20) outliers start: 35 outliers final: 22 residues processed: 202 average time/residue: 0.8632 time to fit residues: 195.3239 Evaluate side-chains 188 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 394 GLU Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 626 MET Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 352 SER Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 173 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 ASN Y 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.128122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.110399 restraints weight = 82599.238| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.35 r_work: 0.3909 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12254 Z= 0.218 Angle : 0.633 7.031 16668 Z= 0.339 Chirality : 0.043 0.172 1934 Planarity : 0.005 0.056 2096 Dihedral : 6.337 55.215 1831 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.28 % Allowed : 16.08 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.66 (0.21), residues: 1510 helix: 1.66 (0.25), residues: 418 sheet: -1.41 (0.28), residues: 311 loop : -1.19 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Y 251 TYR 0.026 0.002 TYR N 95 PHE 0.019 0.002 PHE X 212 TRP 0.018 0.003 TRP Y 99 HIS 0.016 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00489 (12230) covalent geometry : angle 0.62220 (16612) SS BOND : bond 0.00654 ( 16) SS BOND : angle 2.16838 ( 32) hydrogen bonds : bond 0.05973 ( 498) hydrogen bonds : angle 5.18213 ( 1398) link_BETA1-4 : bond 0.00873 ( 1) link_BETA1-4 : angle 2.96753 ( 3) link_NAG-ASN : bond 0.00368 ( 7) link_NAG-ASN : angle 1.71310 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8153 (t) cc_final: 0.7910 (m) REVERT: B 82 SER cc_start: 0.6743 (t) cc_final: 0.6430 (p) REVERT: N 28 THR cc_start: 0.8883 (t) cc_final: 0.8523 (m) REVERT: R 22 MET cc_start: -0.1410 (tpt) cc_final: -0.1873 (mtp) REVERT: R 44 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7662 (pt) REVERT: R 124 GLU cc_start: 0.8149 (tp30) cc_final: 0.7587 (tm-30) REVERT: R 394 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: R 633 ASP cc_start: 0.7475 (t0) cc_final: 0.6901 (m-30) REVERT: Y 126 LEU cc_start: 0.7410 (tt) cc_final: 0.7099 (mp) REVERT: Z 13 ARG cc_start: 0.6657 (mtm110) cc_final: 0.6341 (mtt180) REVERT: Z 38 MET cc_start: 0.6006 (ptt) cc_final: 0.5148 (pp-130) REVERT: Z 42 GLU cc_start: 0.5475 (pt0) cc_final: 0.5050 (pp20) outliers start: 42 outliers final: 28 residues processed: 196 average time/residue: 0.8877 time to fit residues: 194.6014 Evaluate side-chains 183 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 394 GLU Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 626 MET Chi-restraints excluded: chain X residue 34 LYS Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 173 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS Y 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.128300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.110671 restraints weight = 82651.426| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.35 r_work: 0.3929 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12254 Z= 0.145 Angle : 0.572 7.445 16668 Z= 0.305 Chirality : 0.041 0.175 1934 Planarity : 0.004 0.063 2096 Dihedral : 5.889 54.619 1831 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.73 % Allowed : 17.56 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.41 (0.22), residues: 1510 helix: 1.98 (0.26), residues: 419 sheet: -1.31 (0.28), residues: 316 loop : -1.08 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 528 TYR 0.016 0.001 TYR N 95 PHE 0.018 0.001 PHE A 33 TRP 0.016 0.002 TRP Y 211 HIS 0.005 0.001 HIS R 32 Details of bonding type rmsd covalent geometry : bond 0.00325 (12230) covalent geometry : angle 0.56291 (16612) SS BOND : bond 0.00431 ( 16) SS BOND : angle 2.01414 ( 32) hydrogen bonds : bond 0.05271 ( 498) hydrogen bonds : angle 4.94199 ( 1398) link_BETA1-4 : bond 0.00901 ( 1) link_BETA1-4 : angle 2.74439 ( 3) link_NAG-ASN : bond 0.00276 ( 7) link_NAG-ASN : angle 1.35757 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 SER cc_start: 0.6803 (t) cc_final: 0.6509 (p) REVERT: N 28 THR cc_start: 0.8819 (t) cc_final: 0.8421 (m) REVERT: R 22 MET cc_start: -0.1479 (tpt) cc_final: -0.1923 (mtp) REVERT: R 633 ASP cc_start: 0.7466 (t0) cc_final: 0.6832 (m-30) REVERT: Y 9 GLN cc_start: 0.5645 (mm110) cc_final: 0.5436 (tp-100) REVERT: Y 126 LEU cc_start: 0.7387 (tt) cc_final: 0.7079 (mp) REVERT: Z 13 ARG cc_start: 0.6561 (mtm110) cc_final: 0.6246 (mpp-170) REVERT: Z 38 MET cc_start: 0.5864 (ptt) cc_final: 0.5051 (pp-130) REVERT: Z 42 GLU cc_start: 0.5299 (pt0) cc_final: 0.4889 (pp20) outliers start: 35 outliers final: 25 residues processed: 184 average time/residue: 0.8384 time to fit residues: 173.8068 Evaluate side-chains 178 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 691 ILE Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 352 SER Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 234 PHE Chi-restraints excluded: chain Z residue 17 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 GLN Y 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.127312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.109605 restraints weight = 82730.522| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.36 r_work: 0.3921 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 12254 Z= 0.160 Angle : 0.583 14.879 16668 Z= 0.310 Chirality : 0.041 0.193 1934 Planarity : 0.004 0.045 2096 Dihedral : 5.874 54.507 1831 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.97 % Allowed : 18.11 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.38 (0.22), residues: 1510 helix: 2.04 (0.26), residues: 419 sheet: -1.27 (0.29), residues: 308 loop : -1.11 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.019 0.001 TYR N 95 PHE 0.015 0.001 PHE Y 199 TRP 0.015 0.002 TRP Y 211 HIS 0.015 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00363 (12230) covalent geometry : angle 0.57324 (16612) SS BOND : bond 0.00489 ( 16) SS BOND : angle 2.10270 ( 32) hydrogen bonds : bond 0.05281 ( 498) hydrogen bonds : angle 4.89442 ( 1398) link_BETA1-4 : bond 0.00851 ( 1) link_BETA1-4 : angle 2.66646 ( 3) link_NAG-ASN : bond 0.00294 ( 7) link_NAG-ASN : angle 1.43381 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8050 (t) cc_final: 0.7723 (m) REVERT: B 82 SER cc_start: 0.6750 (t) cc_final: 0.6467 (p) REVERT: N 28 THR cc_start: 0.8813 (t) cc_final: 0.8423 (m) REVERT: R 22 MET cc_start: -0.1440 (tpt) cc_final: -0.1887 (mtp) REVERT: R 633 ASP cc_start: 0.7432 (t0) cc_final: 0.6803 (m-30) REVERT: X 378 ASP cc_start: 0.6480 (m-30) cc_final: 0.5990 (m-30) REVERT: Y 13 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5750 (mp10) REVERT: Y 32 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6403 (pt0) REVERT: Y 66 ASP cc_start: 0.6112 (p0) cc_final: 0.5848 (p0) REVERT: Y 126 LEU cc_start: 0.7378 (tt) cc_final: 0.7050 (mp) REVERT: Z 38 MET cc_start: 0.5802 (ptt) cc_final: 0.5025 (pp-130) REVERT: Z 42 GLU cc_start: 0.5302 (pt0) cc_final: 0.4892 (pp20) outliers start: 38 outliers final: 27 residues processed: 182 average time/residue: 0.8568 time to fit residues: 175.2389 Evaluate side-chains 181 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 352 SER Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 13 GLN Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 173 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 2 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 121 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.126054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.108162 restraints weight = 82010.419| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.39 r_work: 0.3935 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12254 Z= 0.132 Angle : 0.562 13.574 16668 Z= 0.298 Chirality : 0.041 0.164 1934 Planarity : 0.004 0.040 2096 Dihedral : 5.688 54.440 1831 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.42 % Allowed : 19.13 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.26 (0.22), residues: 1510 helix: 2.14 (0.26), residues: 413 sheet: -1.21 (0.29), residues: 313 loop : -0.99 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 528 TYR 0.016 0.001 TYR N 95 PHE 0.015 0.001 PHE Y 234 TRP 0.015 0.002 TRP Y 211 HIS 0.018 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00300 (12230) covalent geometry : angle 0.55346 (16612) SS BOND : bond 0.00429 ( 16) SS BOND : angle 1.89059 ( 32) hydrogen bonds : bond 0.05012 ( 498) hydrogen bonds : angle 4.81271 ( 1398) link_BETA1-4 : bond 0.00972 ( 1) link_BETA1-4 : angle 2.61084 ( 3) link_NAG-ASN : bond 0.00260 ( 7) link_NAG-ASN : angle 1.30985 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.6958 (tp40) cc_final: 0.6362 (mp-120) REVERT: A 85 SER cc_start: 0.8090 (t) cc_final: 0.7765 (m) REVERT: B 82 SER cc_start: 0.6732 (t) cc_final: 0.6464 (p) REVERT: N 28 THR cc_start: 0.8775 (t) cc_final: 0.8387 (m) REVERT: R 22 MET cc_start: -0.1481 (tpt) cc_final: -0.1892 (mtp) REVERT: R 633 ASP cc_start: 0.7446 (t0) cc_final: 0.6831 (m-30) REVERT: Y 66 ASP cc_start: 0.6125 (p0) cc_final: 0.5841 (p0) REVERT: Y 82 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.6003 (m100) REVERT: Z 17 GLU cc_start: 0.6981 (tp30) cc_final: 0.6681 (tp30) REVERT: Z 38 MET cc_start: 0.5807 (ptt) cc_final: 0.5051 (pp-130) REVERT: Z 42 GLU cc_start: 0.5324 (pt0) cc_final: 0.4908 (pp20) outliers start: 31 outliers final: 24 residues processed: 180 average time/residue: 0.8318 time to fit residues: 168.9040 Evaluate side-chains 178 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 352 SER Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 234 PHE Chi-restraints excluded: chain Y residue 254 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.128081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.110171 restraints weight = 82649.233| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.35 r_work: 0.3883 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12254 Z= 0.250 Angle : 0.669 13.162 16668 Z= 0.358 Chirality : 0.043 0.168 1934 Planarity : 0.005 0.056 2096 Dihedral : 6.208 54.286 1831 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.20 % Allowed : 18.11 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.60 (0.22), residues: 1510 helix: 1.85 (0.26), residues: 409 sheet: -1.24 (0.29), residues: 307 loop : -1.28 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Y 251 TYR 0.025 0.002 TYR N 95 PHE 0.018 0.002 PHE Y 199 TRP 0.019 0.003 TRP Y 82 HIS 0.008 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00561 (12230) covalent geometry : angle 0.66062 (16612) SS BOND : bond 0.00559 ( 16) SS BOND : angle 1.85976 ( 32) hydrogen bonds : bond 0.06099 ( 498) hydrogen bonds : angle 5.09978 ( 1398) link_BETA1-4 : bond 0.00955 ( 1) link_BETA1-4 : angle 3.09520 ( 3) link_NAG-ASN : bond 0.00476 ( 7) link_NAG-ASN : angle 1.81284 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8128 (t) cc_final: 0.7809 (m) REVERT: B 82 SER cc_start: 0.6808 (t) cc_final: 0.6498 (p) REVERT: N 28 THR cc_start: 0.8860 (t) cc_final: 0.8499 (m) REVERT: R 22 MET cc_start: -0.1250 (tpt) cc_final: -0.1835 (mmt) REVERT: R 633 ASP cc_start: 0.7486 (t0) cc_final: 0.6835 (m-30) REVERT: X 378 ASP cc_start: 0.6656 (m-30) cc_final: 0.6084 (m-30) REVERT: Y 82 TRP cc_start: 0.7768 (OUTLIER) cc_final: 0.6120 (m100) REVERT: Z 13 ARG cc_start: 0.6199 (mtt180) cc_final: 0.5979 (ptp-170) REVERT: Z 17 GLU cc_start: 0.7126 (tp30) cc_final: 0.6869 (tp30) REVERT: Z 38 MET cc_start: 0.5869 (ptt) cc_final: 0.5096 (pp-130) REVERT: Z 42 GLU cc_start: 0.5308 (pt0) cc_final: 0.4970 (pp20) outliers start: 41 outliers final: 31 residues processed: 188 average time/residue: 0.8927 time to fit residues: 188.2151 Evaluate side-chains 181 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 691 ILE Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 352 SER Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 187 VAL Chi-restraints excluded: chain Y residue 234 PHE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Y residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 51 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.124261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.106186 restraints weight = 82008.256| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.39 r_work: 0.3902 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12254 Z= 0.189 Angle : 0.633 12.363 16668 Z= 0.336 Chirality : 0.042 0.167 1934 Planarity : 0.005 0.048 2096 Dihedral : 6.054 54.392 1831 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.50 % Allowed : 19.44 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.57 (0.22), residues: 1510 helix: 1.85 (0.26), residues: 415 sheet: -1.15 (0.29), residues: 309 loop : -1.29 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 60 TYR 0.021 0.002 TYR N 95 PHE 0.016 0.002 PHE Y 199 TRP 0.017 0.002 TRP Y 99 HIS 0.018 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00423 (12230) covalent geometry : angle 0.62558 (16612) SS BOND : bond 0.00486 ( 16) SS BOND : angle 1.73725 ( 32) hydrogen bonds : bond 0.05693 ( 498) hydrogen bonds : angle 5.00680 ( 1398) link_BETA1-4 : bond 0.00578 ( 1) link_BETA1-4 : angle 2.67299 ( 3) link_NAG-ASN : bond 0.00351 ( 7) link_NAG-ASN : angle 1.60254 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8061 (t) cc_final: 0.7776 (m) REVERT: B 82 SER cc_start: 0.6716 (t) cc_final: 0.6468 (p) REVERT: N 28 THR cc_start: 0.8817 (t) cc_final: 0.8455 (m) REVERT: R 22 MET cc_start: -0.1299 (tpt) cc_final: -0.1842 (mmt) REVERT: R 414 TYR cc_start: 0.6733 (m-80) cc_final: 0.6283 (m-80) REVERT: R 633 ASP cc_start: 0.7453 (t0) cc_final: 0.6870 (m-30) REVERT: X 378 ASP cc_start: 0.6560 (m-30) cc_final: 0.5937 (m-30) REVERT: Z 13 ARG cc_start: 0.6323 (mtt180) cc_final: 0.6044 (ptp-170) REVERT: Z 17 GLU cc_start: 0.6948 (tp30) cc_final: 0.6721 (tp30) REVERT: Z 38 MET cc_start: 0.5945 (ptt) cc_final: 0.5179 (pp-130) REVERT: Z 42 GLU cc_start: 0.5405 (pt0) cc_final: 0.5069 (pp20) outliers start: 32 outliers final: 28 residues processed: 177 average time/residue: 0.9084 time to fit residues: 179.4333 Evaluate side-chains 176 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 552 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 691 ILE Chi-restraints excluded: chain X residue 297 LEU Chi-restraints excluded: chain X residue 352 SER Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 187 VAL Chi-restraints excluded: chain Y residue 234 PHE Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 96 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.125060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.107098 restraints weight = 81627.407| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.38 r_work: 0.3926 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12254 Z= 0.133 Angle : 0.569 10.697 16668 Z= 0.302 Chirality : 0.041 0.164 1934 Planarity : 0.004 0.040 2096 Dihedral : 5.688 54.144 1831 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.87 % Allowed : 20.14 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.36 (0.22), residues: 1510 helix: 2.16 (0.26), residues: 409 sheet: -1.22 (0.29), residues: 324 loop : -1.12 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 528 TYR 0.017 0.001 TYR N 95 PHE 0.015 0.001 PHE Y 199 TRP 0.016 0.002 TRP Y 211 HIS 0.008 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00296 (12230) covalent geometry : angle 0.56337 (16612) SS BOND : bond 0.00398 ( 16) SS BOND : angle 1.53534 ( 32) hydrogen bonds : bond 0.05066 ( 498) hydrogen bonds : angle 4.82217 ( 1398) link_BETA1-4 : bond 0.01051 ( 1) link_BETA1-4 : angle 2.59987 ( 3) link_NAG-ASN : bond 0.00288 ( 7) link_NAG-ASN : angle 1.32682 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8688.78 seconds wall clock time: 147 minutes 28.22 seconds (8848.22 seconds total)