Starting phenix.real_space_refine on Fri Jun 20 10:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9i_25758/06_2025/7t9i_25758_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9i_25758/06_2025/7t9i_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_25758/06_2025/7t9i_25758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9i_25758/06_2025/7t9i_25758.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9i_25758/06_2025/7t9i_25758_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9i_25758/06_2025/7t9i_25758_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 2, 'GLU:plan': 1, '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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 10} 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: 13.04, per 1000 atoms: 0.55 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: 5.82 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.85 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: 9.23 Time building geometry restraints manager: 7.15 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: 138.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.430 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 52.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.790 ------------------------------------------------------------------------------- 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 : 3.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP Y 339 HIS 0.005 0.001 HIS Y 225 PHE 0.039 0.002 PHE Z 61 TYR 0.018 0.002 TYR Y 124 ARG 0.026 0.001 ARG B 13 Details of bonding type rmsd link_NAG-ASN : bond 0.05215 ( 7) link_NAG-ASN : angle 4.99401 ( 21) link_BETA1-4 : bond 0.00661 ( 1) link_BETA1-4 : angle 4.96460 ( 3) hydrogen bonds : bond 0.14151 ( 498) hydrogen bonds : angle 6.94786 ( 1398) SS BOND : bond 0.00563 ( 16) SS BOND : angle 1.84455 ( 32) covalent geometry : bond 0.00531 (12230) covalent geometry : angle 0.91492 (16612) *********************** 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 : 1.741 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: 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: 0.7256 (p) REVERT: Y 126 LEU cc_start: 0.6777 (tt) cc_final: 0.6471 (mp) REVERT: Y 127 LYS cc_start: 0.5767 (mttm) cc_final: 0.5141 (ptpp) REVERT: Z 26 ASP cc_start: 0.6184 (p0) cc_final: 0.5836 (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: 1.9685 time to fit residues: 594.4191 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 : 1.810 ------------------------------------------------------------------------------- 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 125 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.0050 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.133909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.116658 restraints weight = 83921.992| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.37 r_work: 0.4013 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12254 Z= 0.190 Angle : 0.621 5.721 16668 Z= 0.333 Chirality : 0.043 0.170 1934 Planarity : 0.005 0.065 2096 Dihedral : 6.366 53.695 1833 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.87 % Allowed : 10.62 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1510 helix: 1.89 (0.25), residues: 415 sheet: -1.18 (0.29), residues: 294 loop : -0.58 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP Y 82 HIS 0.004 0.001 HIS X 362 PHE 0.020 0.002 PHE X 212 TYR 0.014 0.002 TYR B 59 ARG 0.009 0.001 ARG Y 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 7) link_NAG-ASN : angle 1.68531 ( 21) link_BETA1-4 : bond 0.00917 ( 1) link_BETA1-4 : angle 3.33001 ( 3) hydrogen bonds : bond 0.05921 ( 498) hydrogen bonds : angle 5.41349 ( 1398) SS BOND : bond 0.00383 ( 16) SS BOND : angle 1.27152 ( 32) covalent geometry : bond 0.00411 (12230) covalent geometry : angle 0.61466 (16612) *********************** 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 204 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 2.027 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: 0.6666 (t) cc_final: 0.6408 (p) REVERT: R 22 MET cc_start: -0.1729 (tpt) cc_final: -0.2175 (mtp) REVERT: R 394 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: R 434 PHE cc_start: 0.8079 (t80) cc_final: 0.7776 (t80) REVERT: R 510 TYR cc_start: 0.7968 (t80) cc_final: 0.7768 (t80) REVERT: R 572 MET cc_start: 0.5335 (mmm) cc_final: 0.5077 (mtt) REVERT: R 681 PHE cc_start: 0.6568 (m-10) cc_final: 0.5977 (m-80) REVERT: X 378 ASP cc_start: 0.6279 (m-30) cc_final: 0.5868 (m-30) REVERT: Y 105 TYR cc_start: 0.6898 (t80) cc_final: 0.6659 (t80) REVERT: Y 126 LEU cc_start: 0.7074 (tt) cc_final: 0.6767 (mp) REVERT: Y 127 LYS cc_start: 0.5892 (mttm) cc_final: 0.4932 (ptpp) REVERT: Z 26 ASP cc_start: 0.6096 (p0) cc_final: 0.5821 (p0) REVERT: Z 38 MET cc_start: 0.5836 (ptt) cc_final: 0.4913 (pp-130) outliers start: 24 outliers final: 11 residues processed: 197 average time/residue: 1.9678 time to fit residues: 434.8181 Evaluate side-chains 168 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 2.944 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 0.0770 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 ** Y 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.129898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.112304 restraints weight = 82834.730| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.34 r_work: 0.3939 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12254 Z= 0.229 Angle : 0.653 6.656 16668 Z= 0.350 Chirality : 0.044 0.168 1934 Planarity : 0.005 0.060 2096 Dihedral : 6.388 57.085 1831 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.26 % Allowed : 13.82 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), residues: 1510 helix: 1.62 (0.25), residues: 424 sheet: -1.29 (0.28), residues: 306 loop : -1.02 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP Y 82 HIS 0.007 0.001 HIS X 362 PHE 0.023 0.002 PHE X 212 TYR 0.018 0.002 TYR R 279 ARG 0.009 0.001 ARG X 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 7) link_NAG-ASN : angle 1.86724 ( 21) link_BETA1-4 : bond 0.01291 ( 1) link_BETA1-4 : angle 3.08947 ( 3) hydrogen bonds : bond 0.06203 ( 498) hydrogen bonds : angle 5.27751 ( 1398) SS BOND : bond 0.00358 ( 16) SS BOND : angle 1.23733 ( 32) covalent geometry : bond 0.00507 (12230) covalent geometry : angle 0.64688 (16612) *********************** 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 207 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.913 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: 0.6684 (t) cc_final: 0.6372 (p) REVERT: N 28 THR cc_start: 0.8840 (t) cc_final: 0.8477 (m) REVERT: R 22 MET cc_start: -0.1715 (tpt) cc_final: -0.2090 (mtp) REVERT: R 44 ILE cc_start: 0.7903 (pt) cc_final: 0.7329 (pt) REVERT: R 394 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6644 (pm20) REVERT: R 414 TYR cc_start: 0.6711 (m-80) cc_final: 0.6306 (m-80) REVERT: R 510 TYR cc_start: 0.8029 (t80) cc_final: 0.7735 (t80) REVERT: R 633 ASP cc_start: 0.7408 (t0) cc_final: 0.6852 (m-30) REVERT: Y 105 TYR cc_start: 0.6970 (t80) cc_final: 0.6712 (t80) REVERT: Y 126 LEU cc_start: 0.7364 (tt) cc_final: 0.7031 (mp) REVERT: Y 127 LYS cc_start: 0.5976 (mttm) cc_final: 0.5233 (ptpp) REVERT: Z 13 ARG cc_start: 0.6686 (mtm110) cc_final: 0.6308 (ptp-170) REVERT: Z 26 ASP cc_start: 0.5841 (p0) cc_final: 0.5593 (p0) REVERT: Z 38 MET cc_start: 0.5955 (ptt) cc_final: 0.5044 (pp-130) outliers start: 29 outliers final: 15 residues processed: 196 average time/residue: 1.8731 time to fit residues: 415.2959 Evaluate side-chains 184 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.789 ------------------------------------------------------------------------------- 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 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 59 TYR Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 TRP 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 113 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.130128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.112404 restraints weight = 83436.318| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.36 r_work: 0.3948 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12254 Z= 0.162 Angle : 0.572 5.883 16668 Z= 0.306 Chirality : 0.041 0.163 1934 Planarity : 0.004 0.041 2096 Dihedral : 6.039 55.870 1831 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.95 % Allowed : 16.39 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1510 helix: 1.78 (0.25), residues: 425 sheet: -1.29 (0.28), residues: 305 loop : -1.00 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 82 HIS 0.007 0.001 HIS A 90 PHE 0.015 0.001 PHE X 212 TYR 0.013 0.001 TYR R 476 ARG 0.004 0.000 ARG B 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 7) link_NAG-ASN : angle 1.42409 ( 21) link_BETA1-4 : bond 0.00654 ( 1) link_BETA1-4 : angle 2.84593 ( 3) hydrogen bonds : bond 0.05479 ( 498) hydrogen bonds : angle 5.04801 ( 1398) SS BOND : bond 0.00343 ( 16) SS BOND : angle 1.42022 ( 32) covalent geometry : bond 0.00357 (12230) covalent geometry : angle 0.56634 (16612) *********************** 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 205 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.997 Fit side-chains 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: 0.6389 (p) REVERT: N 28 THR cc_start: 0.8816 (t) cc_final: 0.8441 (m) REVERT: R 22 MET cc_start: -0.1617 (tpt) cc_final: -0.1995 (mtp) REVERT: R 394 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: R 414 TYR cc_start: 0.6740 (m-80) cc_final: 0.6324 (m-80) REVERT: R 510 TYR cc_start: 0.7954 (t80) cc_final: 0.7729 (t80) REVERT: R 633 ASP cc_start: 0.7422 (t0) cc_final: 0.6875 (m-30) REVERT: Y 9 GLN cc_start: 0.5693 (mm110) cc_final: 0.5348 (tp-100) REVERT: Y 44 GLN cc_start: 0.7223 (pp30) cc_final: 0.6912 (mp10) REVERT: Y 45 MET cc_start: 0.6025 (mtt) cc_final: 0.5793 (mtt) REVERT: Y 126 LEU cc_start: 0.7333 (tt) cc_final: 0.6985 (mp) REVERT: Y 127 LYS cc_start: 0.5917 (mttm) cc_final: 0.5283 (ptpp) REVERT: Z 38 MET cc_start: 0.5949 (ptt) cc_final: 0.5068 (pp-130) outliers start: 25 outliers final: 16 residues processed: 198 average time/residue: 1.8299 time to fit residues: 410.3291 Evaluate side-chains 177 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 69 THR 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 26 ILE 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 97 SER Chi-restraints excluded: chain Y residue 112 VAL 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 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 187 ASN Y 13 GLN ** Y 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.129290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.111544 restraints weight = 82639.964| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.37 r_work: 0.3936 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 12254 Z= 0.177 Angle : 0.590 8.853 16668 Z= 0.314 Chirality : 0.042 0.167 1934 Planarity : 0.005 0.043 2096 Dihedral : 6.002 55.371 1831 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.73 % Allowed : 16.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1510 helix: 1.87 (0.26), residues: 424 sheet: -1.30 (0.29), residues: 301 loop : -1.06 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 82 HIS 0.006 0.001 HIS A 90 PHE 0.016 0.001 PHE Y 199 TYR 0.018 0.001 TYR N 95 ARG 0.003 0.000 ARG B 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 7) link_NAG-ASN : angle 1.56353 ( 21) link_BETA1-4 : bond 0.00842 ( 1) link_BETA1-4 : angle 2.83954 ( 3) hydrogen bonds : bond 0.05489 ( 498) hydrogen bonds : angle 5.00229 ( 1398) SS BOND : bond 0.00572 ( 16) SS BOND : angle 2.32856 ( 32) covalent geometry : bond 0.00398 (12230) covalent geometry : angle 0.57788 (16612) *********************** 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 203 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 SER cc_start: 0.6666 (t) cc_final: 0.6385 (p) REVERT: N 28 THR cc_start: 0.8809 (t) cc_final: 0.8436 (m) REVERT: R 22 MET cc_start: -0.1610 (tpt) cc_final: -0.2026 (mtp) REVERT: R 44 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7557 (pt) REVERT: R 394 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: R 510 TYR cc_start: 0.7961 (t80) cc_final: 0.7717 (t80) REVERT: R 633 ASP cc_start: 0.7435 (t0) cc_final: 0.6868 (m-30) REVERT: Y 126 LEU cc_start: 0.7343 (tt) cc_final: 0.7081 (mp) REVERT: Y 127 LYS cc_start: 0.5915 (mttm) cc_final: 0.5311 (ptpp) REVERT: Z 13 ARG cc_start: 0.6718 (mtm110) cc_final: 0.6453 (mtt180) REVERT: Z 38 MET cc_start: 0.5950 (ptt) cc_final: 0.5128 (pp-130) REVERT: Z 42 GLU cc_start: 0.5424 (pt0) cc_final: 0.5092 (pp20) outliers start: 35 outliers final: 22 residues processed: 195 average time/residue: 1.7877 time to fit residues: 393.4944 Evaluate side-chains 183 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 SER 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 44 ILE Chi-restraints excluded: chain R residue 56 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 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 81 ILE 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 173 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN Y 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.126730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.109087 restraints weight = 82613.845| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.34 r_work: 0.3921 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 12254 Z= 0.195 Angle : 0.615 12.228 16668 Z= 0.328 Chirality : 0.042 0.173 1934 Planarity : 0.005 0.046 2096 Dihedral : 6.087 55.088 1831 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.28 % Allowed : 16.86 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1510 helix: 1.82 (0.25), residues: 424 sheet: -1.14 (0.29), residues: 307 loop : -1.16 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 99 HIS 0.006 0.001 HIS R 32 PHE 0.017 0.002 PHE X 212 TYR 0.018 0.002 TYR N 95 ARG 0.003 0.000 ARG X 231 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 7) link_NAG-ASN : angle 1.61584 ( 21) link_BETA1-4 : bond 0.00546 ( 1) link_BETA1-4 : angle 2.80738 ( 3) hydrogen bonds : bond 0.05632 ( 498) hydrogen bonds : angle 5.00244 ( 1398) SS BOND : bond 0.00444 ( 16) SS BOND : angle 1.91957 ( 32) covalent geometry : bond 0.00437 (12230) covalent geometry : angle 0.60593 (16612) *********************** 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 203 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7889 (m) REVERT: B 82 SER cc_start: 0.6729 (t) cc_final: 0.6464 (p) REVERT: N 28 THR cc_start: 0.8803 (t) cc_final: 0.8429 (m) REVERT: R 22 MET cc_start: -0.1473 (tpt) cc_final: -0.1895 (mtp) REVERT: R 40 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7176 (p) REVERT: R 44 ILE cc_start: 0.7907 (pt) cc_final: 0.7551 (pt) REVERT: R 124 GLU cc_start: 0.8107 (tp30) cc_final: 0.7554 (tm-30) REVERT: R 394 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: R 510 TYR cc_start: 0.7990 (t80) cc_final: 0.7729 (t80) REVERT: R 633 ASP cc_start: 0.7394 (t0) cc_final: 0.6842 (m-30) REVERT: Y 126 LEU cc_start: 0.7414 (tt) cc_final: 0.7099 (mp) REVERT: Z 13 ARG cc_start: 0.6659 (mtm110) cc_final: 0.6305 (mpp-170) REVERT: Z 38 MET cc_start: 0.5998 (ptt) cc_final: 0.5191 (pp-130) REVERT: Z 42 GLU cc_start: 0.5530 (pt0) cc_final: 0.5115 (pp20) outliers start: 42 outliers final: 29 residues processed: 191 average time/residue: 1.9242 time to fit residues: 421.9909 Evaluate side-chains 186 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain R residue 40 THR 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 394 GLU 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 626 MET 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 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 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 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 130 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN Y 13 GLN Y 32 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 = 0.4314 r_free = 0.4314 target = 0.126027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.108253 restraints weight = 83073.694| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.38 r_work: 0.3899 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 12254 Z= 0.216 Angle : 0.629 12.215 16668 Z= 0.336 Chirality : 0.043 0.165 1934 Planarity : 0.005 0.049 2096 Dihedral : 6.169 54.723 1831 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.12 % Allowed : 18.27 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1510 helix: 1.83 (0.26), residues: 416 sheet: -1.16 (0.29), residues: 305 loop : -1.24 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP Y 99 HIS 0.006 0.001 HIS A 90 PHE 0.017 0.002 PHE X 212 TYR 0.019 0.002 TYR N 95 ARG 0.004 0.001 ARG Y 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 7) link_NAG-ASN : angle 1.70802 ( 21) link_BETA1-4 : bond 0.01047 ( 1) link_BETA1-4 : angle 2.98235 ( 3) hydrogen bonds : bond 0.05884 ( 498) hydrogen bonds : angle 5.05203 ( 1398) SS BOND : bond 0.00562 ( 16) SS BOND : angle 1.92784 ( 32) covalent geometry : bond 0.00483 (12230) covalent geometry : angle 0.62034 (16612) *********************** 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 200 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 1.927 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: 0.8079 (t) cc_final: 0.7846 (m) REVERT: B 82 SER cc_start: 0.6737 (t) cc_final: 0.6470 (p) REVERT: N 28 THR cc_start: 0.8827 (t) cc_final: 0.8457 (m) REVERT: R 22 MET cc_start: -0.1352 (tpt) cc_final: -0.1821 (mtp) REVERT: R 72 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: R 394 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: R 414 TYR cc_start: 0.6759 (m-80) cc_final: 0.6296 (m-80) REVERT: R 510 TYR cc_start: 0.7998 (t80) cc_final: 0.7682 (t80) REVERT: R 633 ASP cc_start: 0.7446 (t0) cc_final: 0.6864 (m-30) REVERT: X 378 ASP cc_start: 0.6610 (m-30) cc_final: 0.6063 (m-30) REVERT: Z 38 MET cc_start: 0.6016 (ptt) cc_final: 0.5203 (pp-130) REVERT: Z 42 GLU cc_start: 0.5458 (pt0) cc_final: 0.5103 (pp20) outliers start: 40 outliers final: 28 residues processed: 186 average time/residue: 1.6501 time to fit residues: 349.5271 Evaluate side-chains 184 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 56 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 104 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 R residue 691 ILE Chi-restraints excluded: chain X residue 20 ARG 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 254 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN Y 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.124206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.106194 restraints weight = 81821.784| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.38 r_work: 0.3894 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12254 Z= 0.203 Angle : 0.622 11.339 16668 Z= 0.333 Chirality : 0.042 0.167 1934 Planarity : 0.005 0.048 2096 Dihedral : 6.146 54.514 1831 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.36 % Allowed : 18.35 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1510 helix: 1.84 (0.26), residues: 416 sheet: -1.16 (0.29), residues: 306 loop : -1.25 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP Y 99 HIS 0.006 0.001 HIS R 32 PHE 0.017 0.002 PHE Y 199 TYR 0.019 0.002 TYR N 95 ARG 0.003 0.000 ARG B 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 7) link_NAG-ASN : angle 1.65429 ( 21) link_BETA1-4 : bond 0.00920 ( 1) link_BETA1-4 : angle 2.86920 ( 3) hydrogen bonds : bond 0.05829 ( 498) hydrogen bonds : angle 5.03367 ( 1398) SS BOND : bond 0.00525 ( 16) SS BOND : angle 1.74836 ( 32) covalent geometry : bond 0.00455 (12230) covalent geometry : angle 0.61438 (16612) *********************** 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 202 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 2.552 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: 0.6785 (t) cc_final: 0.6494 (p) REVERT: N 28 THR cc_start: 0.8827 (t) cc_final: 0.8456 (m) REVERT: R 22 MET cc_start: -0.1146 (tpt) cc_final: -0.1708 (mtp) REVERT: R 124 GLU cc_start: 0.8209 (tp30) cc_final: 0.7616 (tm-30) REVERT: R 394 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6493 (pm20) REVERT: R 414 TYR cc_start: 0.6762 (m-80) cc_final: 0.6301 (m-80) REVERT: R 510 TYR cc_start: 0.7962 (t80) cc_final: 0.7667 (t80) REVERT: R 633 ASP cc_start: 0.7478 (t0) cc_final: 0.6833 (m-30) REVERT: Y 32 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6347 (pt0) REVERT: Z 38 MET cc_start: 0.5873 (ptt) cc_final: 0.5082 (pp-130) REVERT: Z 42 GLU cc_start: 0.5260 (pt0) cc_final: 0.4930 (pp20) outliers start: 43 outliers final: 28 residues processed: 189 average time/residue: 1.7803 time to fit residues: 380.7287 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 : 1.798 ------------------------------------------------------------------------------- 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 85 SER 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 91 GLN Chi-restraints excluded: chain R residue 104 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 598 CYS Chi-restraints excluded: chain R residue 626 MET 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 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 Chi-restraints excluded: chain Y residue 187 VAL Chi-restraints excluded: chain Y residue 234 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.123330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.105336 restraints weight = 81787.230| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.38 r_work: 0.3884 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12254 Z= 0.225 Angle : 0.649 10.451 16668 Z= 0.346 Chirality : 0.043 0.171 1934 Planarity : 0.005 0.052 2096 Dihedral : 6.250 54.257 1831 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.97 % Allowed : 19.13 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1510 helix: 1.74 (0.26), residues: 415 sheet: -1.18 (0.29), residues: 304 loop : -1.37 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP Y 99 HIS 0.007 0.001 HIS R 32 PHE 0.017 0.002 PHE X 212 TYR 0.020 0.002 TYR N 95 ARG 0.003 0.001 ARG X 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 7) link_NAG-ASN : angle 1.76708 ( 21) link_BETA1-4 : bond 0.00901 ( 1) link_BETA1-4 : angle 2.89590 ( 3) hydrogen bonds : bond 0.06077 ( 498) hydrogen bonds : angle 5.09800 ( 1398) SS BOND : bond 0.00525 ( 16) SS BOND : angle 1.61488 ( 32) covalent geometry : bond 0.00503 (12230) covalent geometry : angle 0.64155 (16612) *********************** 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 192 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.797 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: 0.8114 (t) cc_final: 0.7782 (m) REVERT: B 82 SER cc_start: 0.6775 (t) cc_final: 0.6507 (p) REVERT: N 28 THR cc_start: 0.8858 (t) cc_final: 0.8504 (m) REVERT: R 22 MET cc_start: -0.1201 (tpt) cc_final: -0.1769 (mmt) REVERT: R 112 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7071 (ptm160) REVERT: R 153 PHE cc_start: 0.7717 (m-80) cc_final: 0.7492 (m-10) REVERT: R 394 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: R 414 TYR cc_start: 0.6750 (m-80) cc_final: 0.6301 (m-80) REVERT: R 510 TYR cc_start: 0.7972 (t80) cc_final: 0.7655 (t80) REVERT: R 633 ASP cc_start: 0.7445 (t0) cc_final: 0.6808 (m-30) REVERT: X 378 ASP cc_start: 0.6623 (m-30) cc_final: 0.6205 (m-30) REVERT: Y 66 ASP cc_start: 0.6008 (p0) cc_final: 0.5648 (p0) REVERT: Z 38 MET cc_start: 0.5866 (ptt) cc_final: 0.5080 (pp-130) REVERT: Z 42 GLU cc_start: 0.5317 (pt0) cc_final: 0.4978 (pp20) outliers start: 38 outliers final: 28 residues processed: 182 average time/residue: 1.7506 time to fit residues: 359.3622 Evaluate side-chains 182 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 56 THR Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 112 ARG 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 598 CYS Chi-restraints excluded: chain R residue 626 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 86 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN Y 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.124337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.106452 restraints weight = 82054.365| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.38 r_work: 0.3905 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12254 Z= 0.149 Angle : 0.596 10.205 16668 Z= 0.317 Chirality : 0.042 0.170 1934 Planarity : 0.005 0.044 2096 Dihedral : 5.981 54.385 1831 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.26 % Allowed : 19.83 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1510 helix: 1.93 (0.26), residues: 415 sheet: -1.21 (0.29), residues: 308 loop : -1.25 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 211 HIS 0.008 0.001 HIS R 32 PHE 0.016 0.001 PHE Y 199 TYR 0.016 0.001 TYR N 95 ARG 0.004 0.000 ARG R 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 7) link_NAG-ASN : angle 1.53545 ( 21) link_BETA1-4 : bond 0.01196 ( 1) link_BETA1-4 : angle 2.70575 ( 3) hydrogen bonds : bond 0.05472 ( 498) hydrogen bonds : angle 4.94418 ( 1398) SS BOND : bond 0.00413 ( 16) SS BOND : angle 1.50193 ( 32) covalent geometry : bond 0.00330 (12230) covalent geometry : angle 0.58985 (16612) ********************** 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: 29 poor density : 155 time to evaluate : 2.052 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: 0.8060 (t) cc_final: 0.7727 (m) REVERT: B 82 SER cc_start: 0.6699 (t) cc_final: 0.6457 (p) REVERT: N 28 THR cc_start: 0.8809 (t) cc_final: 0.8431 (m) REVERT: R 22 MET cc_start: -0.1091 (tpt) cc_final: -0.1682 (mmt) REVERT: R 124 GLU cc_start: 0.8161 (tp30) cc_final: 0.7664 (tm-30) REVERT: R 153 PHE cc_start: 0.7685 (m-80) cc_final: 0.7468 (m-10) REVERT: R 414 TYR cc_start: 0.6739 (m-80) cc_final: 0.6281 (m-80) REVERT: R 633 ASP cc_start: 0.7462 (t0) cc_final: 0.6818 (m-30) REVERT: X 20 ARG cc_start: 0.6844 (tpp-160) cc_final: 0.6636 (ptm-80) REVERT: X 378 ASP cc_start: 0.6562 (m-30) cc_final: 0.6028 (m-30) REVERT: Y 66 ASP cc_start: 0.5953 (p0) cc_final: 0.5615 (p0) REVERT: Y 82 TRP cc_start: 0.7615 (OUTLIER) cc_final: 0.6013 (m100) REVERT: Z 38 MET cc_start: 0.5827 (ptt) cc_final: 0.5072 (pp-130) REVERT: Z 42 GLU cc_start: 0.5322 (pt0) cc_final: 0.4976 (pp20) outliers start: 29 outliers final: 25 residues processed: 179 average time/residue: 1.8399 time to fit residues: 375.5613 Evaluate side-chains 178 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 76 VAL 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 86 ASP Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 426 LEU 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 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 112 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.128255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.110475 restraints weight = 82521.708| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.35 r_work: 0.3896 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12254 Z= 0.192 Angle : 0.625 10.872 16668 Z= 0.331 Chirality : 0.042 0.169 1934 Planarity : 0.005 0.047 2096 Dihedral : 6.024 54.071 1831 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.50 % Allowed : 20.14 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1510 helix: 1.87 (0.26), residues: 415 sheet: -1.21 (0.29), residues: 308 loop : -1.31 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 99 HIS 0.005 0.001 HIS A 90 PHE 0.017 0.002 PHE Y 199 TYR 0.018 0.002 TYR N 95 ARG 0.003 0.000 ARG Y 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 1.62476 ( 21) link_BETA1-4 : bond 0.01106 ( 1) link_BETA1-4 : angle 2.82171 ( 3) hydrogen bonds : bond 0.05691 ( 498) hydrogen bonds : angle 4.96950 ( 1398) SS BOND : bond 0.00439 ( 16) SS BOND : angle 2.30754 ( 32) covalent geometry : bond 0.00431 (12230) covalent geometry : angle 0.61367 (16612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18965.98 seconds wall clock time: 324 minutes 45.27 seconds (19485.27 seconds total)