Starting phenix.real_space_refine on Fri Jun 20 18:18:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utz_26795/06_2025/7utz_26795_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utz_26795/06_2025/7utz_26795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7utz_26795/06_2025/7utz_26795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utz_26795/06_2025/7utz_26795.map" model { file = "/net/cci-nas-00/data/ceres_data/7utz_26795/06_2025/7utz_26795_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utz_26795/06_2025/7utz_26795_trim.cif" } resolution = 2.4 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= 0.026 sd= 0.080 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 7680 2.51 5 N 2039 2.21 5 O 2228 1.98 5 H 11632 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23679 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1273 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1648 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 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: 9460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9460 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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: "A" 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: "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: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'NAG': 4, 'Z41': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.18, per 1000 atoms: 0.56 Number of scatterers: 23679 At special positions: 0 Unit cell: (177.834, 133.791, 108.03, 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 2228 8.00 N 2039 7.00 C 7680 6.00 H 11632 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 95 " distance=2.03 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 284 " - pdb=" SG CYS R 408 " distance=2.03 Simple disulfide: pdb=" SG CYS R 301 " - pdb=" SG CYS R 390 " distance=2.03 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 NAG-ASN " NAG A 101 " - " ASN A 78 " " NAG A 102 " - " ASN A 52 " " NAG B 201 " - " ASN B 23 " " 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: 7.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 19 sheets defined 32.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.697A pdb=" N SER B 48 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.633A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix 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: 3.777A pdb=" N LEU R 175 " --> pdb=" O PHE R 172 " (cutoff:3.500A) removed outlier: 4.263A 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: 4.387A pdb=" N PHE R 221 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.521A pdb=" N LYS R 287 " --> pdb=" O CYS R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 305 removed outlier: 3.856A pdb=" N SER R 305 " --> pdb=" O CYS R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 391 Processing helix chain 'R' and resid 416 through 442 removed outlier: 4.683A 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: 3.715A pdb=" N HIS R 484 " --> pdb=" O GLU R 480 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ILE R 486 " --> pdb=" O TYR R 482 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 525 removed outlier: 4.068A 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 Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 576 through 609 Processing helix chain 'R' and resid 620 through 649 removed outlier: 3.895A 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: 3.725A pdb=" N LYS R 660 " --> pdb=" O VAL R 656 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 3.907A 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 40 Processing helix chain 'X' and resid 52 through 59 Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.516A 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: 3.571A 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: 4.015A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE X 345 " --> pdb=" O ILE X 341 " (cutoff:3.500A) removed outlier: 4.001A 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 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: 3.639A 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 'B' and resid 3 through 11 removed outlier: 3.510A pdb=" N LEU B 20 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N THR B 25 " --> pdb=" O PRO A 38 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS B 31 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS A 32 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE B 96 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER A 55 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 69 removed outlier: 6.432A pdb=" N ALA A 81 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 65 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS A 79 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG A 67 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A 77 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 69 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 75 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 63 removed outlier: 6.892A pdb=" N SER B 82 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE B 57 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA B 80 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 59 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR B 61 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 76 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU B 63 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR B 74 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.533A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN N 39 " --> pdb=" O VAL N 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 30 through 33 removed outlier: 3.668A pdb=" N ARG R 38 " --> pdb=" O HIS R 32 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU R 57 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N SER R 84 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU R 59 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR R 111 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR R 136 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN R 110 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU R 131 " --> pdb=" O GLU R 157 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR R 159 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE R 133 " --> pdb=" O THR R 159 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE R 154 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LYS R 183 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU R 156 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU R 180 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA R 204 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N LEU R 230 " --> pdb=" O LYS R 201 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP R 203 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA R 275 " --> pdb=" O THR R 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.231A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 166 through 167 Processing sheet with id=AB3, first strand: chain 'X' and resid 210 through 214 removed outlier: 7.201A pdb=" N ARG X 42 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE X 245 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU X 44 " --> pdb=" O ILE X 245 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL X 247 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU X 46 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP X 249 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 46 through 51 removed outlier: 6.554A pdb=" N ILE Y 338 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR Y 50 " --> pdb=" O LEU Y 336 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU Y 336 " --> pdb=" O THR Y 50 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS Y 317 " --> pdb=" O GLY Y 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.707A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS Y 78 " --> pdb=" O SER Y 74 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS Y 89 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 100 through 105 removed outlier: 6.733A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE Y 123 " --> pdb=" O SER Y 136 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG Y 134 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 146 through 151 removed outlier: 3.571A pdb=" N CYS Y 148 " --> pdb=" O SER Y 160 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.022A 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: 7.086A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA Y 208 " --> pdb=" O THR Y 221 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR Y 221 " --> pdb=" O ALA Y 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU Y 210 " --> pdb=" O ARG Y 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 233 through 234 removed outlier: 6.623A pdb=" N CYS Y 250 " --> pdb=" O THR Y 263 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR Y 263 " --> pdb=" O CYS Y 250 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU Y 252 " --> pdb=" O LEU Y 261 " (cutoff:3.500A) removed outlier: 3.558A 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: 6.417A pdb=" N CYS Y 294 " --> pdb=" O VAL Y 307 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL Y 307 " --> pdb=" O CYS Y 294 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL Y 296 " --> pdb=" O ALA Y 305 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1377 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: 9.41 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11598 1.04 - 1.23: 822 1.23 - 1.43: 4503 1.43 - 1.63: 6882 1.63 - 1.83: 132 Bond restraints: 23937 Sorted by residual: bond pdb=" N GLY X 304 " pdb=" CA GLY X 304 " ideal model delta sigma weight residual 1.448 1.494 -0.045 1.43e-02 4.89e+03 1.00e+01 bond pdb=" N GLY R 21 " pdb=" CA GLY R 21 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 bond pdb=" C ALA X 303 " pdb=" N GLY X 304 " ideal model delta sigma weight residual 1.331 1.359 -0.028 1.32e-02 5.74e+03 4.44e+00 bond pdb=" N GLY X 353 " pdb=" CA GLY X 353 " ideal model delta sigma weight residual 1.449 1.477 -0.027 1.45e-02 4.76e+03 3.56e+00 bond pdb=" C ALA B 72 " pdb=" N PRO B 73 " ideal model delta sigma weight residual 1.336 1.353 -0.018 9.80e-03 1.04e+04 3.21e+00 ... (remaining 23932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 42360 2.06 - 4.12: 578 4.12 - 6.18: 73 6.18 - 8.24: 4 8.24 - 10.30: 1 Bond angle restraints: 43016 Sorted by residual: angle pdb=" N SER R 26 " pdb=" CA SER R 26 " pdb=" C SER R 26 " ideal model delta sigma weight residual 108.13 111.50 -3.37 9.00e-01 1.23e+00 1.40e+01 angle pdb=" C30 Z41 R 805 " pdb=" C31 Z41 R 805 " pdb=" C32 Z41 R 805 " ideal model delta sigma weight residual 114.63 104.33 10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C ALA X 303 " pdb=" N GLY X 304 " pdb=" CA GLY X 304 " ideal model delta sigma weight residual 121.07 126.56 -5.49 1.79e+00 3.12e-01 9.40e+00 angle pdb=" C PRO N 102 " pdb=" N PHE N 103 " pdb=" CA PHE N 103 " ideal model delta sigma weight residual 121.70 126.96 -5.26 1.80e+00 3.09e-01 8.55e+00 angle pdb=" CA TRP X 234 " pdb=" CB TRP X 234 " pdb=" CG TRP X 234 " ideal model delta sigma weight residual 113.60 119.05 -5.45 1.90e+00 2.77e-01 8.21e+00 ... (remaining 43011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10456 17.94 - 35.88: 812 35.88 - 53.82: 208 53.82 - 71.76: 50 71.76 - 89.70: 22 Dihedral angle restraints: 11548 sinusoidal: 6188 harmonic: 5360 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 -35.35 -50.65 1 1.00e+01 1.00e-02 3.51e+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 -134.08 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA SER X 352 " pdb=" C SER X 352 " pdb=" N GLY X 353 " pdb=" CA GLY X 353 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 11545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1476 0.047 - 0.093: 349 0.093 - 0.140: 104 0.140 - 0.187: 6 0.187 - 0.233: 1 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CA GLU X 27 " pdb=" N GLU X 27 " pdb=" C GLU X 27 " pdb=" CB GLU X 27 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA CYS A 7 " pdb=" N CYS A 7 " pdb=" C CYS A 7 " pdb=" CB CYS A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE R 47 " pdb=" N ILE R 47 " pdb=" C ILE R 47 " pdb=" CB ILE R 47 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1933 not shown) Planarity restraints: 3579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER X 352 " 0.035 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C SER X 352 " -0.121 2.00e-02 2.50e+03 pdb=" O SER X 352 " 0.046 2.00e-02 2.50e+03 pdb=" N GLY X 353 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 303 " 0.034 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" C ALA X 303 " -0.117 2.00e-02 2.50e+03 pdb=" O ALA X 303 " 0.044 2.00e-02 2.50e+03 pdb=" N GLY X 304 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER X 352 " 0.016 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" N GLY X 353 " -0.050 2.00e-02 2.50e+03 pdb=" CA GLY X 353 " 0.013 2.00e-02 2.50e+03 pdb=" H GLY X 353 " 0.022 2.00e-02 2.50e+03 ... (remaining 3576 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 3345 2.27 - 2.85: 53434 2.85 - 3.44: 62469 3.44 - 4.02: 87418 4.02 - 4.60: 131738 Nonbonded interactions: 338404 Sorted by model distance: nonbonded pdb=" O LEU X 44 " pdb=" H ILE X 245 " model vdw 1.689 2.450 nonbonded pdb="HD21 ASN X 23 " pdb=" OE1 GLU X 27 " model vdw 1.704 2.450 nonbonded pdb="HD22 ASN Y 230 " pdb=" OD1 ASP Y 246 " model vdw 1.716 2.450 nonbonded pdb=" O ALA R 254 " pdb=" HG SER R 278 " model vdw 1.720 2.450 nonbonded pdb=" OD1 ASP R 160 " pdb="HD21 ASN R 186 " model vdw 1.723 2.450 ... (remaining 338399 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: 4.470 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: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 55.080 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 : 0.004 0.045 12329 Z= 0.186 Angle : 0.697 10.300 16753 Z= 0.362 Chirality : 0.044 0.233 1936 Planarity : 0.005 0.077 2104 Dihedral : 12.457 81.074 4519 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.05 (0.21), residues: 1514 helix: 1.63 (0.25), residues: 431 sheet: -1.13 (0.28), residues: 322 loop : -0.43 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 234 HIS 0.005 0.001 HIS Y 311 PHE 0.018 0.001 PHE Y 235 TYR 0.015 0.001 TYR R 667 ARG 0.016 0.001 ARG B 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 7) link_NAG-ASN : angle 1.56363 ( 21) hydrogen bonds : bond 0.17739 ( 496) hydrogen bonds : angle 7.30517 ( 1377) SS BOND : bond 0.00319 ( 17) SS BOND : angle 1.32197 ( 34) covalent geometry : bond 0.00399 (12305) covalent geometry : angle 0.69376 (16698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 244 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8204 (t) cc_final: 0.7897 (m) REVERT: B 50 ASP cc_start: 0.5881 (p0) cc_final: 0.5378 (p0) REVERT: N 28 THR cc_start: 0.8411 (t) cc_final: 0.8019 (m) REVERT: N 114 THR cc_start: 0.8070 (p) cc_final: 0.7845 (t) REVERT: R 45 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6376 (tp-100) REVERT: R 98 TYR cc_start: 0.6942 (t80) cc_final: 0.6666 (t80) REVERT: R 274 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7280 (mtp85) REVERT: R 437 LEU cc_start: 0.7303 (pp) cc_final: 0.6912 (mt) REVERT: R 688 ASP cc_start: 0.6794 (m-30) cc_final: 0.6480 (m-30) REVERT: Y 35 ASN cc_start: 0.6518 (m-40) cc_final: 0.6152 (m110) REVERT: Y 110 ASN cc_start: 0.6764 (m-40) cc_final: 0.6376 (t0) REVERT: Y 259 GLN cc_start: 0.6891 (tt0) cc_final: 0.6493 (pt0) REVERT: Y 334 SER cc_start: 0.7907 (p) cc_final: 0.7668 (m) REVERT: Z 46 LYS cc_start: 0.7841 (mppt) cc_final: 0.7004 (pttm) REVERT: Z 47 GLU cc_start: 0.6925 (pm20) cc_final: 0.6221 (pp20) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 2.4972 time to fit residues: 666.5387 Evaluate side-chains 159 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 125 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Z 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.138146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.122328 restraints weight = 59676.753| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.71 r_work: 0.3908 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12329 Z= 0.188 Angle : 0.580 6.172 16753 Z= 0.312 Chirality : 0.043 0.299 1936 Planarity : 0.005 0.063 2104 Dihedral : 6.991 59.862 1857 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.09 % Allowed : 9.64 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.02 (0.21), residues: 1514 helix: 1.89 (0.25), residues: 431 sheet: -1.30 (0.27), residues: 342 loop : -0.37 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Y 82 HIS 0.004 0.001 HIS R 32 PHE 0.025 0.002 PHE R 500 TYR 0.012 0.001 TYR R 481 ARG 0.009 0.001 ARG X 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 7) link_NAG-ASN : angle 1.78861 ( 21) hydrogen bonds : bond 0.04657 ( 496) hydrogen bonds : angle 5.37967 ( 1377) SS BOND : bond 0.00346 ( 17) SS BOND : angle 1.39475 ( 34) covalent geometry : bond 0.00415 (12305) covalent geometry : angle 0.57416 (16698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 194 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASP cc_start: 0.6618 (p0) cc_final: 0.6142 (p0) REVERT: N 3 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6950 (tm-30) REVERT: N 28 THR cc_start: 0.8897 (t) cc_final: 0.8521 (m) REVERT: R 45 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6844 (mm-40) REVERT: R 396 MET cc_start: 0.7984 (tmt) cc_final: 0.7508 (tmt) REVERT: R 437 LEU cc_start: 0.7406 (pp) cc_final: 0.6944 (mt) REVERT: R 609 ARG cc_start: 0.5656 (ttt-90) cc_final: 0.5375 (tpt-90) REVERT: R 688 ASP cc_start: 0.6959 (m-30) cc_final: 0.6649 (m-30) REVERT: Y 35 ASN cc_start: 0.6763 (m-40) cc_final: 0.6360 (m110) REVERT: Y 46 ARG cc_start: 0.6581 (mmm160) cc_final: 0.6273 (mmm160) REVERT: Y 72 SER cc_start: 0.8133 (t) cc_final: 0.7912 (m) REVERT: Y 110 ASN cc_start: 0.7260 (m-40) cc_final: 0.6932 (t0) REVERT: Y 215 GLU cc_start: 0.7101 (pm20) cc_final: 0.6877 (pm20) REVERT: Y 258 ASP cc_start: 0.7572 (t0) cc_final: 0.7186 (t0) REVERT: Z 46 LYS cc_start: 0.7872 (mppt) cc_final: 0.7127 (pttm) REVERT: Z 47 GLU cc_start: 0.7236 (pm20) cc_final: 0.6437 (pp20) outliers start: 14 outliers final: 8 residues processed: 190 average time/residue: 2.5483 time to fit residues: 533.5789 Evaluate side-chains 173 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 125 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN N 120 GLN Z 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.129396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.113528 restraints weight = 59244.959| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.70 r_work: 0.3837 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 12329 Z= 0.300 Angle : 0.684 11.385 16753 Z= 0.366 Chirality : 0.045 0.283 1936 Planarity : 0.006 0.080 2104 Dihedral : 7.897 61.257 1857 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.02 % Allowed : 11.12 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.39 (0.21), residues: 1514 helix: 1.68 (0.25), residues: 419 sheet: -1.43 (0.27), residues: 327 loop : -0.76 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Y 82 HIS 0.008 0.002 HIS A 83 PHE 0.018 0.002 PHE R 416 TYR 0.025 0.002 TYR Y 264 ARG 0.008 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 7) link_NAG-ASN : angle 2.37312 ( 21) hydrogen bonds : bond 0.05196 ( 496) hydrogen bonds : angle 5.31748 ( 1377) SS BOND : bond 0.00458 ( 17) SS BOND : angle 2.19997 ( 34) covalent geometry : bond 0.00668 (12305) covalent geometry : angle 0.67242 (16698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 201 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 VAL cc_start: 0.6886 (OUTLIER) cc_final: 0.6657 (t) REVERT: N 28 THR cc_start: 0.8970 (t) cc_final: 0.8636 (m) REVERT: R 38 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7676 (mtp85) REVERT: R 404 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: R 609 ARG cc_start: 0.5765 (OUTLIER) cc_final: 0.5510 (tpt-90) REVERT: R 688 ASP cc_start: 0.7126 (m-30) cc_final: 0.6746 (m-30) REVERT: Y 35 ASN cc_start: 0.6847 (m-40) cc_final: 0.6451 (m110) REVERT: Y 110 ASN cc_start: 0.7494 (m-40) cc_final: 0.7099 (m-40) REVERT: Y 112 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7697 (t) REVERT: Y 334 SER cc_start: 0.8259 (p) cc_final: 0.8025 (m) REVERT: Z 47 GLU cc_start: 0.7066 (pm20) cc_final: 0.6163 (pp20) outliers start: 26 outliers final: 10 residues processed: 191 average time/residue: 2.7536 time to fit residues: 574.7448 Evaluate side-chains 177 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 404 GLU Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain R residue 609 ARG Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 254 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 0.0770 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.135153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.119285 restraints weight = 59825.587| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.71 r_work: 0.3855 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12329 Z= 0.189 Angle : 0.574 7.932 16753 Z= 0.308 Chirality : 0.042 0.225 1936 Planarity : 0.005 0.074 2104 Dihedral : 7.438 59.868 1855 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 12.13 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.21 (0.21), residues: 1514 helix: 1.94 (0.25), residues: 419 sheet: -1.45 (0.26), residues: 326 loop : -0.66 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 234 HIS 0.005 0.001 HIS R 32 PHE 0.013 0.002 PHE R 631 TYR 0.015 0.001 TYR R 482 ARG 0.008 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 7) link_NAG-ASN : angle 1.69768 ( 21) hydrogen bonds : bond 0.04435 ( 496) hydrogen bonds : angle 5.06821 ( 1377) SS BOND : bond 0.00341 ( 17) SS BOND : angle 1.62475 ( 34) covalent geometry : bond 0.00419 (12305) covalent geometry : angle 0.56681 (16698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 198 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 2.021 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: N 28 THR cc_start: 0.8942 (t) cc_final: 0.8602 (m) REVERT: N 58 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7660 (mp) REVERT: R 609 ARG cc_start: 0.5703 (OUTLIER) cc_final: 0.5432 (tpt-90) REVERT: R 688 ASP cc_start: 0.7153 (m-30) cc_final: 0.6762 (m-30) REVERT: Y 35 ASN cc_start: 0.6830 (m-40) cc_final: 0.6372 (m110) REVERT: Y 46 ARG cc_start: 0.6627 (mmm160) cc_final: 0.6236 (mmm160) REVERT: Y 110 ASN cc_start: 0.7449 (m-40) cc_final: 0.7090 (m-40) REVERT: Y 112 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7689 (t) REVERT: Y 334 SER cc_start: 0.8249 (p) cc_final: 0.8016 (m) REVERT: Z 47 GLU cc_start: 0.7125 (pm20) cc_final: 0.6139 (pp20) outliers start: 27 outliers final: 10 residues processed: 192 average time/residue: 2.5916 time to fit residues: 543.8261 Evaluate side-chains 176 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 583 ILE Chi-restraints excluded: chain R residue 609 ARG Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain Y residue 280 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.133559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.117870 restraints weight = 59940.883| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.67 r_work: 0.3831 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 12329 Z= 0.258 Angle : 0.628 10.164 16753 Z= 0.337 Chirality : 0.044 0.232 1936 Planarity : 0.005 0.080 2104 Dihedral : 7.504 63.142 1855 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.72 % Allowed : 12.29 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.34 (0.21), residues: 1514 helix: 1.84 (0.25), residues: 419 sheet: -1.46 (0.27), residues: 326 loop : -0.78 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP Y 82 HIS 0.006 0.001 HIS A 83 PHE 0.018 0.002 PHE R 631 TYR 0.018 0.002 TYR R 481 ARG 0.012 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 7) link_NAG-ASN : angle 2.20473 ( 21) hydrogen bonds : bond 0.04705 ( 496) hydrogen bonds : angle 5.11771 ( 1377) SS BOND : bond 0.00430 ( 17) SS BOND : angle 2.02132 ( 34) covalent geometry : bond 0.00572 (12305) covalent geometry : angle 0.61774 (16698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.936 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: N 28 THR cc_start: 0.8936 (t) cc_final: 0.8620 (m) REVERT: N 58 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7741 (mp) REVERT: R 609 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5518 (tpt-90) REVERT: R 688 ASP cc_start: 0.7233 (m-30) cc_final: 0.6914 (m-30) REVERT: Y 35 ASN cc_start: 0.6904 (m-40) cc_final: 0.6469 (m110) REVERT: Y 110 ASN cc_start: 0.7471 (m-40) cc_final: 0.7129 (m-40) REVERT: Z 47 GLU cc_start: 0.7103 (pm20) cc_final: 0.6185 (pp20) outliers start: 35 outliers final: 20 residues processed: 195 average time/residue: 2.8459 time to fit residues: 609.4081 Evaluate side-chains 190 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain R residue 583 ILE Chi-restraints excluded: chain R residue 609 ARG Chi-restraints excluded: chain X residue 27 GLU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 235 PHE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Y residue 280 LYS Chi-restraints excluded: chain Z residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 125 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.118471 restraints weight = 59034.780| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.70 r_work: 0.3841 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12329 Z= 0.204 Angle : 0.586 8.968 16753 Z= 0.314 Chirality : 0.042 0.218 1936 Planarity : 0.005 0.084 2104 Dihedral : 7.311 63.857 1855 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.94 % Allowed : 14.31 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.28 (0.21), residues: 1514 helix: 1.94 (0.25), residues: 420 sheet: -1.45 (0.27), residues: 313 loop : -0.79 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 234 HIS 0.005 0.001 HIS R 32 PHE 0.021 0.002 PHE R 631 TYR 0.014 0.002 TYR R 481 ARG 0.011 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 7) link_NAG-ASN : angle 1.89686 ( 21) hydrogen bonds : bond 0.04415 ( 496) hydrogen bonds : angle 4.99234 ( 1377) SS BOND : bond 0.00387 ( 17) SS BOND : angle 1.79842 ( 34) covalent geometry : bond 0.00450 (12305) covalent geometry : angle 0.57767 (16698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 ARG cc_start: 0.7796 (mmt90) cc_final: 0.7567 (mpt-90) REVERT: N 28 THR cc_start: 0.8917 (t) cc_final: 0.8615 (m) REVERT: N 58 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7713 (mp) REVERT: R 38 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7632 (mtp85) REVERT: R 490 THR cc_start: 0.7149 (m) cc_final: 0.6895 (m) REVERT: R 609 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.5400 (tpt-90) REVERT: R 688 ASP cc_start: 0.7204 (m-30) cc_final: 0.6908 (m-30) REVERT: Y 35 ASN cc_start: 0.6884 (m-40) cc_final: 0.6446 (m110) REVERT: Y 46 ARG cc_start: 0.6637 (mmm160) cc_final: 0.6358 (mmp-170) REVERT: Y 110 ASN cc_start: 0.7462 (m-40) cc_final: 0.7107 (m-40) REVERT: Y 235 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7686 (t80) REVERT: Y 258 ASP cc_start: 0.7685 (t0) cc_final: 0.7246 (t0) REVERT: Y 334 SER cc_start: 0.8262 (p) cc_final: 0.8037 (m) REVERT: Z 47 GLU cc_start: 0.7126 (pm20) cc_final: 0.6139 (pp20) outliers start: 25 outliers final: 15 residues processed: 193 average time/residue: 2.6172 time to fit residues: 554.3029 Evaluate side-chains 191 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain R residue 583 ILE Chi-restraints excluded: chain R residue 609 ARG Chi-restraints excluded: chain X residue 27 GLU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 235 PHE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Y residue 280 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.135210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.119506 restraints weight = 59672.134| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.69 r_work: 0.3859 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12329 Z= 0.152 Angle : 0.546 7.524 16753 Z= 0.291 Chirality : 0.041 0.183 1936 Planarity : 0.005 0.091 2104 Dihedral : 7.067 63.844 1855 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.87 % Allowed : 15.40 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.11 (0.22), residues: 1514 helix: 2.17 (0.25), residues: 420 sheet: -1.43 (0.27), residues: 312 loop : -0.70 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 234 HIS 0.010 0.001 HIS R 478 PHE 0.022 0.001 PHE R 631 TYR 0.013 0.001 TYR R 476 ARG 0.014 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 7) link_NAG-ASN : angle 1.62352 ( 21) hydrogen bonds : bond 0.04104 ( 496) hydrogen bonds : angle 4.83034 ( 1377) SS BOND : bond 0.00318 ( 17) SS BOND : angle 1.53863 ( 34) covalent geometry : bond 0.00335 (12305) covalent geometry : angle 0.53923 (16698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 195 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.873 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: N 28 THR cc_start: 0.8909 (t) cc_final: 0.8613 (m) REVERT: R 38 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7627 (mtp85) REVERT: R 50 LEU cc_start: 0.7743 (mp) cc_final: 0.7452 (mp) REVERT: R 404 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: R 490 THR cc_start: 0.7161 (m) cc_final: 0.6906 (m) REVERT: R 688 ASP cc_start: 0.7188 (m-30) cc_final: 0.6889 (m-30) REVERT: Y 35 ASN cc_start: 0.6876 (m-40) cc_final: 0.6437 (m-40) REVERT: Y 46 ARG cc_start: 0.6637 (mmm160) cc_final: 0.6355 (mmp-170) REVERT: Y 110 ASN cc_start: 0.7435 (m-40) cc_final: 0.7084 (m-40) REVERT: Y 235 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7729 (t80) REVERT: Y 258 ASP cc_start: 0.7641 (t0) cc_final: 0.7265 (t0) REVERT: Y 334 SER cc_start: 0.8229 (p) cc_final: 0.7990 (m) REVERT: Z 47 GLU cc_start: 0.7201 (pm20) cc_final: 0.6250 (pp20) outliers start: 24 outliers final: 14 residues processed: 187 average time/residue: 2.8210 time to fit residues: 578.9098 Evaluate side-chains 187 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 404 GLU Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain R residue 583 ILE Chi-restraints excluded: chain X residue 27 GLU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 235 PHE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Y residue 280 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN X 29 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 = 0.4143 r_free = 0.4143 target = 0.132939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.117477 restraints weight = 59474.239| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.66 r_work: 0.3821 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 12329 Z= 0.295 Angle : 0.663 10.007 16753 Z= 0.355 Chirality : 0.045 0.223 1936 Planarity : 0.005 0.062 2104 Dihedral : 7.623 67.018 1855 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.11 % Allowed : 14.93 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.39 (0.21), residues: 1514 helix: 1.78 (0.25), residues: 420 sheet: -1.45 (0.27), residues: 320 loop : -0.84 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Y 82 HIS 0.006 0.001 HIS R 478 PHE 0.029 0.002 PHE R 631 TYR 0.019 0.002 TYR R 482 ARG 0.009 0.001 ARG B 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00828 ( 7) link_NAG-ASN : angle 2.39778 ( 21) hydrogen bonds : bond 0.04829 ( 496) hydrogen bonds : angle 5.10237 ( 1377) SS BOND : bond 0.00559 ( 17) SS BOND : angle 1.99146 ( 34) covalent geometry : bond 0.00657 (12305) covalent geometry : angle 0.65246 (16698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 212 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7482 (mpt-90) REVERT: B 58 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7303 (tp) REVERT: N 28 THR cc_start: 0.8912 (t) cc_final: 0.8628 (m) REVERT: R 38 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7627 (mtp85) REVERT: R 50 LEU cc_start: 0.7808 (mp) cc_final: 0.7502 (mp) REVERT: R 404 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6731 (tt0) REVERT: R 416 PHE cc_start: 0.8019 (p90) cc_final: 0.7693 (p90) REVERT: R 421 VAL cc_start: 0.7855 (t) cc_final: 0.7626 (p) REVERT: R 490 THR cc_start: 0.7351 (m) cc_final: 0.7091 (m) REVERT: Y 35 ASN cc_start: 0.6879 (m-40) cc_final: 0.6449 (m110) REVERT: Y 235 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7984 (t80) REVERT: Y 258 ASP cc_start: 0.7683 (t0) cc_final: 0.7259 (t0) REVERT: Z 47 GLU cc_start: 0.7152 (pm20) cc_final: 0.6124 (pp20) outliers start: 40 outliers final: 21 residues processed: 197 average time/residue: 2.3463 time to fit residues: 508.7151 Evaluate side-chains 191 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 404 GLU Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain R residue 583 ILE Chi-restraints excluded: chain X residue 27 GLU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 235 PHE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain Y residue 280 LYS Chi-restraints excluded: chain Z residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Y 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.134769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.119073 restraints weight = 59157.915| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.69 r_work: 0.3847 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12329 Z= 0.178 Angle : 0.583 6.884 16753 Z= 0.310 Chirality : 0.042 0.171 1936 Planarity : 0.005 0.076 2104 Dihedral : 7.234 67.095 1855 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.18 % Allowed : 15.71 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.25 (0.21), residues: 1514 helix: 1.92 (0.25), residues: 420 sheet: -1.44 (0.27), residues: 309 loop : -0.76 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 169 HIS 0.008 0.001 HIS R 478 PHE 0.020 0.001 PHE R 631 TYR 0.018 0.001 TYR R 482 ARG 0.019 0.001 ARG X 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 7) link_NAG-ASN : angle 1.77333 ( 21) hydrogen bonds : bond 0.04271 ( 496) hydrogen bonds : angle 4.90138 ( 1377) SS BOND : bond 0.00364 ( 17) SS BOND : angle 1.46169 ( 34) covalent geometry : bond 0.00392 (12305) covalent geometry : angle 0.57649 (16698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 195 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.904 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: B 58 ILE cc_start: 0.7723 (pp) cc_final: 0.7244 (tp) REVERT: N 28 THR cc_start: 0.8909 (t) cc_final: 0.8623 (m) REVERT: R 38 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7606 (mtp85) REVERT: R 50 LEU cc_start: 0.7803 (mp) cc_final: 0.7518 (mp) REVERT: R 404 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6706 (tt0) REVERT: R 490 THR cc_start: 0.7322 (m) cc_final: 0.7062 (m) REVERT: Y 35 ASN cc_start: 0.6882 (m-40) cc_final: 0.6448 (m-40) REVERT: Y 258 ASP cc_start: 0.7599 (t0) cc_final: 0.7286 (t0) REVERT: Y 334 SER cc_start: 0.8266 (p) cc_final: 0.8027 (m) REVERT: Z 47 GLU cc_start: 0.7263 (pm20) cc_final: 0.6281 (pp20) outliers start: 28 outliers final: 21 residues processed: 186 average time/residue: 2.4822 time to fit residues: 506.1550 Evaluate side-chains 186 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 404 GLU Chi-restraints excluded: chain R residue 465 MET Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 583 ILE Chi-restraints excluded: chain X residue 27 GLU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Y residue 280 LYS Chi-restraints excluded: chain Z residue 21 MET Chi-restraints excluded: chain Z residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Y 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.119045 restraints weight = 59345.632| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.69 r_work: 0.3846 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12329 Z= 0.187 Angle : 0.585 8.274 16753 Z= 0.312 Chirality : 0.042 0.188 1936 Planarity : 0.005 0.066 2104 Dihedral : 7.148 67.969 1855 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.10 % Allowed : 16.10 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.23 (0.22), residues: 1514 helix: 1.97 (0.25), residues: 420 sheet: -1.44 (0.27), residues: 310 loop : -0.75 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 234 HIS 0.007 0.001 HIS R 478 PHE 0.015 0.001 PHE R 631 TYR 0.019 0.002 TYR R 387 ARG 0.009 0.001 ARG B 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 7) link_NAG-ASN : angle 1.86690 ( 21) hydrogen bonds : bond 0.04282 ( 496) hydrogen bonds : angle 4.87924 ( 1377) SS BOND : bond 0.00388 ( 17) SS BOND : angle 1.66986 ( 34) covalent geometry : bond 0.00413 (12305) covalent geometry : angle 0.57709 (16698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ILE cc_start: 0.7720 (pp) cc_final: 0.7237 (tp) REVERT: N 28 THR cc_start: 0.8908 (t) cc_final: 0.8629 (m) REVERT: R 38 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7615 (mtp85) REVERT: R 50 LEU cc_start: 0.7832 (mp) cc_final: 0.7522 (mp) REVERT: R 404 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6739 (tt0) REVERT: Y 35 ASN cc_start: 0.6882 (m-40) cc_final: 0.6441 (m-40) REVERT: Y 258 ASP cc_start: 0.7629 (t0) cc_final: 0.7282 (t0) REVERT: Y 334 SER cc_start: 0.8261 (p) cc_final: 0.8019 (m) REVERT: Z 47 GLU cc_start: 0.7249 (pm20) cc_final: 0.6268 (pp20) outliers start: 27 outliers final: 20 residues processed: 182 average time/residue: 2.5531 time to fit residues: 511.4062 Evaluate side-chains 188 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 404 GLU Chi-restraints excluded: chain R residue 465 MET Chi-restraints excluded: chain R residue 487 ASP Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 583 ILE Chi-restraints excluded: chain X residue 27 GLU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 98 SER Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Y residue 280 LYS Chi-restraints excluded: chain Z residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Y 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.136041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.120388 restraints weight = 59071.946| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.68 r_work: 0.3854 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12329 Z= 0.169 Angle : 0.569 7.110 16753 Z= 0.303 Chirality : 0.042 0.164 1936 Planarity : 0.004 0.048 2104 Dihedral : 7.035 68.211 1855 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.02 % Allowed : 16.17 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.21 (0.22), residues: 1514 helix: 2.00 (0.25), residues: 420 sheet: -1.45 (0.28), residues: 300 loop : -0.75 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 234 HIS 0.008 0.001 HIS R 478 PHE 0.015 0.001 PHE R 631 TYR 0.015 0.001 TYR R 482 ARG 0.008 0.000 ARG R 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 7) link_NAG-ASN : angle 1.73295 ( 21) hydrogen bonds : bond 0.04161 ( 496) hydrogen bonds : angle 4.81731 ( 1377) SS BOND : bond 0.00328 ( 17) SS BOND : angle 1.47813 ( 34) covalent geometry : bond 0.00373 (12305) covalent geometry : angle 0.56317 (16698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25161.97 seconds wall clock time: 434 minutes 41.22 seconds (26081.22 seconds total)