Starting phenix.real_space_refine on Fri Sep 27 23:44:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/09_2024/6x3w_22035.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/09_2024/6x3w_22035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/09_2024/6x3w_22035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/09_2024/6x3w_22035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/09_2024/6x3w_22035.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/09_2024/6x3w_22035.cif" } resolution = 3.3 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11235 2.51 5 N 2832 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17399 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'ABU': 1, 'NAG': 1, 'UQA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.14, per 1000 atoms: 0.58 Number of scatterers: 17399 At special positions: 0 Unit cell: (141.075, 127.875, 136.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3235 8.00 N 2832 7.00 C 11235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.02 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 505 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 2.1 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 28 sheets defined 31.1% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.880A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 339 removed outlier: 4.080A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.969A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.717A pdb=" N ILE B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.993A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.117A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 277 removed outlier: 3.658A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 345 removed outlier: 3.928A pdb=" N ALA B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 218 through 236 removed outlier: 5.203A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.148A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 268 removed outlier: 4.373A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 4.004A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.840A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 251 through 275 removed outlier: 3.592A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.505A pdb=" N ARG D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 99 through 106 removed outlier: 4.154A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.151A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.572A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 296 through 324 removed outlier: 4.394A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.590A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 3.793A pdb=" N LEU E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.742A pdb=" N ASP J 90 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.716A pdb=" N THR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.573A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.928A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.816A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.207A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.262A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.064A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.786A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.829A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.762A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.485A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.316A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.925A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.925A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.794A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.794A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS E 184 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR E 55 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER E 186 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N MET E 57 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL E 188 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL E 59 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL E 190 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER E 61 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.617A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.435A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.592A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.803A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.779A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.588A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.606A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.721A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.307A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2637 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4373 1.33 - 1.46: 4820 1.46 - 1.58: 8475 1.58 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 17835 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE2 ABU A 405 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CD ABU C 506 " pdb=" OE2 ABU C 506 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C MET D 114 " pdb=" N PRO D 115 " ideal model delta sigma weight residual 1.332 1.374 -0.042 1.12e-02 7.97e+03 1.41e+01 bond pdb=" C VAL D 252 " pdb=" N PRO D 253 " ideal model delta sigma weight residual 1.335 1.373 -0.039 1.28e-02 6.10e+03 9.07e+00 bond pdb=" C THR E 125 " pdb=" N THR E 126 " ideal model delta sigma weight residual 1.333 1.292 0.042 1.39e-02 5.18e+03 8.99e+00 ... (remaining 17830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 23358 2.70 - 5.40: 786 5.40 - 8.10: 92 8.10 - 10.79: 16 10.79 - 13.49: 4 Bond angle restraints: 24256 Sorted by residual: angle pdb=" N ARG C 269 " pdb=" CA ARG C 269 " pdb=" C ARG C 269 " ideal model delta sigma weight residual 113.41 104.73 8.68 1.22e+00 6.72e-01 5.07e+01 angle pdb=" C THR C 271 " pdb=" N LEU C 272 " pdb=" CA LEU C 272 " ideal model delta sigma weight residual 123.96 133.94 -9.98 1.44e+00 4.82e-01 4.80e+01 angle pdb=" N ILE C 322 " pdb=" CA ILE C 322 " pdb=" C ILE C 322 " ideal model delta sigma weight residual 112.96 107.97 4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA GLU C 147 " pdb=" CB GLU C 147 " pdb=" CG GLU C 147 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" N LEU C 152 " pdb=" CA LEU C 152 " pdb=" C LEU C 152 " ideal model delta sigma weight residual 108.34 100.95 7.39 1.64e+00 3.72e-01 2.03e+01 ... (remaining 24251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 10093 21.87 - 43.73: 601 43.73 - 65.60: 64 65.60 - 87.47: 34 87.47 - 109.33: 14 Dihedral angle restraints: 10806 sinusoidal: 4550 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -9.25 -76.75 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -12.15 -73.85 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CA CYS C 150 " pdb=" C CYS C 150 " pdb=" N THR C 151 " pdb=" CA THR C 151 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 10803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 2784 0.283 - 0.565: 9 0.565 - 0.848: 4 0.848 - 1.130: 1 1.130 - 1.413: 1 Chirality restraints: 2799 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.99 -1.41 2.00e-02 2.50e+03 4.99e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.52e+03 chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.64 0.76 2.00e-02 2.50e+03 1.46e+03 ... (remaining 2796 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.193 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG M 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.258 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.180 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG M 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.129 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" C7 NAG G 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.020 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1974 2.75 - 3.29: 15879 3.29 - 3.82: 29623 3.82 - 4.36: 36151 4.36 - 4.90: 63776 Nonbonded interactions: 147403 Sorted by model distance: nonbonded pdb=" OD1 ASP E 120 " pdb=" O4 MAN G 10 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP A 121 " pdb=" OG1 THR A 123 " model vdw 2.269 3.040 nonbonded pdb=" O ALA E 295 " pdb=" OH TYR E 350 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR D 26 " pdb=" OD2 ASP D 72 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.289 3.040 ... (remaining 147398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 340) selection = (chain 'C' and resid 7 through 340) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.120 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.008 0.083 17835 Z= 0.519 Angle : 1.158 13.492 24256 Z= 0.640 Chirality : 0.082 1.413 2799 Planarity : 0.008 0.159 2985 Dihedral : 14.582 109.332 6759 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.85 % Allowed : 6.80 % Favored : 92.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -2.06 (0.16), residues: 2103 helix: -0.16 (0.20), residues: 581 sheet: -1.01 (0.19), residues: 623 loop : -2.41 (0.17), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 103 HIS 0.008 0.002 HIS D 56 PHE 0.031 0.004 PHE C 221 TYR 0.040 0.003 TYR A 157 ARG 0.009 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 411 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8036 (p0) cc_final: 0.7053 (t0) REVERT: A 142 ARG cc_start: 0.7557 (mtp180) cc_final: 0.7157 (mtt180) REVERT: A 274 LYS cc_start: 0.7994 (mttt) cc_final: 0.7761 (mttm) REVERT: A 323 PHE cc_start: 0.7139 (t80) cc_final: 0.6765 (t80) REVERT: C 52 GLU cc_start: 0.7965 (mp0) cc_final: 0.7668 (mp0) REVERT: C 142 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7411 (mtp85) REVERT: C 303 ASN cc_start: 0.8725 (t0) cc_final: 0.8518 (t0) REVERT: D 93 LYS cc_start: 0.8503 (tptp) cc_final: 0.7776 (tptp) REVERT: D 98 ASP cc_start: 0.8287 (p0) cc_final: 0.8048 (p0) REVERT: D 156 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8195 (mtmt) REVERT: E 296 MET cc_start: 0.7496 (ttp) cc_final: 0.7282 (ttp) REVERT: E 298 LEU cc_start: 0.8952 (tp) cc_final: 0.8721 (tt) REVERT: E 301 SER cc_start: 0.8822 (m) cc_final: 0.8179 (m) REVERT: E 305 ILE cc_start: 0.8045 (mm) cc_final: 0.7610 (mm) REVERT: E 337 ILE cc_start: 0.8683 (tp) cc_final: 0.8421 (tp) outliers start: 16 outliers final: 10 residues processed: 421 average time/residue: 0.3282 time to fit residues: 199.9917 Evaluate side-chains 341 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 331 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 274 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 65 GLN A 185 GLN A 303 ASN B 68 GLN B 142 HIS B 189 ASN B 275 ASN B 308 ASN C 41 ASN C 54 ASN C 65 GLN C 185 GLN C 303 ASN D 68 GLN D 102 HIS E 60 ASN E 128 ASN E 163 HIS E 258 ASN E 318 HIS I 79 GLN J 6 GLN L 42 GLN K 6 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17835 Z= 0.215 Angle : 0.601 9.409 24256 Z= 0.307 Chirality : 0.044 0.254 2799 Planarity : 0.004 0.041 2985 Dihedral : 8.194 76.290 2830 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.23 % Allowed : 11.15 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.17 (0.17), residues: 2103 helix: 0.60 (0.21), residues: 588 sheet: -0.66 (0.19), residues: 639 loop : -1.77 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 103 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.002 PHE D 310 TYR 0.022 0.001 TYR A 299 ARG 0.006 0.001 ARG K 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 355 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7128 (mtt180) REVERT: A 323 PHE cc_start: 0.7105 (t80) cc_final: 0.6657 (t80) REVERT: B 17 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7709 (mtt-85) REVERT: B 202 ILE cc_start: 0.9042 (mm) cc_final: 0.8764 (mt) REVERT: B 258 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7290 (t80) REVERT: B 266 MET cc_start: 0.8881 (mmm) cc_final: 0.8670 (mmm) REVERT: C 52 GLU cc_start: 0.7929 (mp0) cc_final: 0.7648 (mp0) REVERT: C 163 ASP cc_start: 0.8243 (m-30) cc_final: 0.7820 (m-30) REVERT: D 93 LYS cc_start: 0.8452 (tptp) cc_final: 0.8003 (mmmm) REVERT: D 156 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8321 (mtmt) REVERT: D 310 PHE cc_start: 0.8427 (m-10) cc_final: 0.8137 (m-10) REVERT: E 296 MET cc_start: 0.7453 (ttp) cc_final: 0.7162 (ttp) REVERT: E 301 SER cc_start: 0.8928 (m) cc_final: 0.8419 (m) REVERT: E 305 ILE cc_start: 0.8314 (mm) cc_final: 0.7855 (mm) REVERT: E 337 ILE cc_start: 0.8672 (tp) cc_final: 0.8357 (tp) REVERT: I 13 MET cc_start: 0.4502 (OUTLIER) cc_final: 0.4069 (ppp) REVERT: K 5 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7106 (tm-30) outliers start: 42 outliers final: 30 residues processed: 375 average time/residue: 0.3286 time to fit residues: 179.6654 Evaluate side-chains 361 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 329 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN A 224 GLN B 116 ASN E 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17835 Z= 0.193 Angle : 0.556 9.663 24256 Z= 0.282 Chirality : 0.043 0.263 2799 Planarity : 0.004 0.038 2985 Dihedral : 6.764 65.665 2822 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 13.33 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.64 (0.18), residues: 2103 helix: 1.09 (0.21), residues: 588 sheet: -0.49 (0.19), residues: 631 loop : -1.37 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 103 HIS 0.010 0.001 HIS B 142 PHE 0.015 0.001 PHE D 310 TYR 0.022 0.001 TYR A 299 ARG 0.007 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 341 time to evaluate : 2.011 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7168 (mtt180) REVERT: A 323 PHE cc_start: 0.7126 (t80) cc_final: 0.6598 (t80) REVERT: B 17 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7695 (mtt-85) REVERT: B 202 ILE cc_start: 0.9028 (mm) cc_final: 0.8799 (mt) REVERT: B 240 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7616 (tp) REVERT: B 258 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7282 (t80) REVERT: B 266 MET cc_start: 0.8942 (mmm) cc_final: 0.8652 (mmm) REVERT: D 15 PHE cc_start: 0.8520 (m-80) cc_final: 0.8066 (m-80) REVERT: D 93 LYS cc_start: 0.8411 (tptp) cc_final: 0.7934 (mmmm) REVERT: D 156 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8311 (mtmt) REVERT: D 310 PHE cc_start: 0.8314 (m-10) cc_final: 0.7212 (m-10) REVERT: D 317 ARG cc_start: 0.6859 (ttt180) cc_final: 0.6565 (ttt180) REVERT: E 296 MET cc_start: 0.7441 (ttp) cc_final: 0.7143 (ttp) REVERT: E 301 SER cc_start: 0.8905 (m) cc_final: 0.8440 (m) REVERT: E 305 ILE cc_start: 0.8369 (mm) cc_final: 0.7918 (mm) REVERT: E 337 ILE cc_start: 0.8664 (tp) cc_final: 0.8364 (tp) REVERT: I 13 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.4184 (ppp) REVERT: J 112 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8511 (t) REVERT: K 5 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7126 (tm-30) REVERT: K 102 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8161 (mmm-85) outliers start: 52 outliers final: 37 residues processed: 369 average time/residue: 0.3141 time to fit residues: 170.5730 Evaluate side-chains 354 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 313 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 308 ASN E 318 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17835 Z= 0.241 Angle : 0.556 9.515 24256 Z= 0.281 Chirality : 0.043 0.255 2799 Planarity : 0.004 0.036 2985 Dihedral : 6.164 56.557 2822 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 13.65 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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 (0.18), residues: 2103 helix: 1.24 (0.21), residues: 596 sheet: -0.47 (0.19), residues: 639 loop : -0.98 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 103 HIS 0.005 0.001 HIS B 142 PHE 0.015 0.001 PHE A 221 TYR 0.022 0.001 TYR A 299 ARG 0.007 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 324 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8604 (ptt) REVERT: A 142 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7239 (mtt180) REVERT: A 224 GLN cc_start: 0.8379 (tt0) cc_final: 0.8091 (tt0) REVERT: A 323 PHE cc_start: 0.7163 (t80) cc_final: 0.6552 (t80) REVERT: B 112 MET cc_start: 0.8266 (tpp) cc_final: 0.8021 (tpp) REVERT: B 240 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7640 (tp) REVERT: B 258 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7221 (t80) REVERT: B 266 MET cc_start: 0.8992 (mmm) cc_final: 0.8686 (mmm) REVERT: B 338 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7947 (mp) REVERT: D 21 ARG cc_start: 0.7160 (ttp-110) cc_final: 0.6891 (ttp-110) REVERT: D 89 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8425 (pt) REVERT: D 93 LYS cc_start: 0.8442 (tptp) cc_final: 0.7973 (mmmm) REVERT: D 156 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8246 (mtmt) REVERT: D 310 PHE cc_start: 0.8294 (m-10) cc_final: 0.7532 (m-10) REVERT: E 276 MET cc_start: 0.8733 (tpp) cc_final: 0.8445 (mmm) REVERT: E 296 MET cc_start: 0.7388 (ttp) cc_final: 0.7072 (ttp) REVERT: E 301 SER cc_start: 0.8947 (m) cc_final: 0.8512 (m) REVERT: E 305 ILE cc_start: 0.8406 (mm) cc_final: 0.7997 (mm) REVERT: E 337 ILE cc_start: 0.8679 (tp) cc_final: 0.8395 (tp) REVERT: E 356 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.5035 (t80) REVERT: I 13 MET cc_start: 0.4692 (OUTLIER) cc_final: 0.4336 (ppp) REVERT: J 112 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8564 (t) REVERT: K 5 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7088 (tm-30) REVERT: K 102 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8288 (mmm-85) outliers start: 65 outliers final: 46 residues processed: 360 average time/residue: 0.3087 time to fit residues: 164.5588 Evaluate side-chains 362 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 308 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 110 GLN Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 185 GLN B 308 ASN D 151 HIS E 318 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17835 Z= 0.257 Angle : 0.560 9.547 24256 Z= 0.285 Chirality : 0.044 0.256 2799 Planarity : 0.004 0.034 2985 Dihedral : 5.901 55.467 2822 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.72 % Allowed : 14.45 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.19 (0.18), residues: 2103 helix: 1.32 (0.21), residues: 595 sheet: -0.47 (0.19), residues: 640 loop : -0.78 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 319 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.002 PHE A 221 TYR 0.023 0.001 TYR A 299 ARG 0.007 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 318 time to evaluate : 2.037 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8603 (ptt) REVERT: A 142 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7333 (mtt180) REVERT: A 224 GLN cc_start: 0.8443 (tt0) cc_final: 0.8069 (tt0) REVERT: A 323 PHE cc_start: 0.7129 (t80) cc_final: 0.6474 (t80) REVERT: B 24 ASP cc_start: 0.6963 (t0) cc_final: 0.6672 (p0) REVERT: B 112 MET cc_start: 0.8117 (tpp) cc_final: 0.7915 (tpp) REVERT: B 240 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7693 (tp) REVERT: B 258 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7214 (t80) REVERT: B 266 MET cc_start: 0.9010 (mmm) cc_final: 0.8677 (mmm) REVERT: D 21 ARG cc_start: 0.7149 (ttp-110) cc_final: 0.6880 (ttp-110) REVERT: D 93 LYS cc_start: 0.8478 (tptp) cc_final: 0.8119 (mmmt) REVERT: D 156 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8263 (mtmt) REVERT: D 209 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7291 (mt-10) REVERT: D 264 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7793 (mm) REVERT: D 310 PHE cc_start: 0.8285 (m-10) cc_final: 0.8015 (m-10) REVERT: E 296 MET cc_start: 0.7354 (ttp) cc_final: 0.6994 (ttp) REVERT: E 301 SER cc_start: 0.8947 (m) cc_final: 0.8491 (m) REVERT: E 305 ILE cc_start: 0.8436 (mm) cc_final: 0.8052 (mm) REVERT: E 337 ILE cc_start: 0.8697 (tp) cc_final: 0.8417 (tp) REVERT: E 356 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.5029 (t80) REVERT: I 13 MET cc_start: 0.4760 (OUTLIER) cc_final: 0.4375 (ppp) REVERT: I 90 GLN cc_start: 0.9259 (pp30) cc_final: 0.9049 (pp30) REVERT: J 112 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8689 (t) REVERT: K 5 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7073 (tm-30) REVERT: K 102 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8301 (mmm-85) outliers start: 70 outliers final: 50 residues processed: 360 average time/residue: 0.3061 time to fit residues: 162.7197 Evaluate side-chains 364 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 307 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 308 ASN E 200 GLN E 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17835 Z= 0.176 Angle : 0.529 9.545 24256 Z= 0.268 Chirality : 0.043 0.255 2799 Planarity : 0.004 0.036 2985 Dihedral : 5.719 56.583 2822 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.51 % Allowed : 15.03 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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 (0.18), residues: 2103 helix: 1.44 (0.21), residues: 594 sheet: -0.39 (0.20), residues: 629 loop : -0.64 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 103 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE A 221 TYR 0.023 0.001 TYR A 299 ARG 0.007 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 326 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8559 (ptt) REVERT: A 142 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7322 (mtt180) REVERT: A 224 GLN cc_start: 0.8415 (tt0) cc_final: 0.8045 (tt0) REVERT: A 323 PHE cc_start: 0.7117 (t80) cc_final: 0.6445 (t80) REVERT: B 17 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7774 (mtt-85) REVERT: B 24 ASP cc_start: 0.6941 (t0) cc_final: 0.6699 (p0) REVERT: B 112 MET cc_start: 0.8098 (tpp) cc_final: 0.7891 (tpp) REVERT: B 240 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7651 (tp) REVERT: B 258 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7190 (t80) REVERT: B 266 MET cc_start: 0.8989 (mmm) cc_final: 0.8640 (mmm) REVERT: D 21 ARG cc_start: 0.7141 (ttp-110) cc_final: 0.6894 (ttp-110) REVERT: D 93 LYS cc_start: 0.8433 (tptp) cc_final: 0.8008 (mmmm) REVERT: D 156 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8259 (mtmt) REVERT: D 164 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7754 (mtp-110) REVERT: D 264 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7797 (mm) REVERT: D 310 PHE cc_start: 0.8299 (m-10) cc_final: 0.8034 (m-10) REVERT: E 98 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8397 (mt) REVERT: E 178 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 276 MET cc_start: 0.8693 (tpp) cc_final: 0.8419 (mmm) REVERT: E 296 MET cc_start: 0.7264 (ttp) cc_final: 0.6962 (ttp) REVERT: E 301 SER cc_start: 0.8953 (m) cc_final: 0.8541 (m) REVERT: E 305 ILE cc_start: 0.8444 (mm) cc_final: 0.8047 (mm) REVERT: E 337 ILE cc_start: 0.8703 (tp) cc_final: 0.8423 (tp) REVERT: E 356 TYR cc_start: 0.5327 (OUTLIER) cc_final: 0.4996 (t80) REVERT: I 13 MET cc_start: 0.4665 (OUTLIER) cc_final: 0.4297 (ppp) REVERT: I 79 GLN cc_start: 0.8130 (mp10) cc_final: 0.7202 (mp10) REVERT: J 112 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (t) REVERT: L 79 GLN cc_start: 0.7583 (mp10) cc_final: 0.7295 (mp10) REVERT: K 102 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8299 (mmm-85) outliers start: 66 outliers final: 44 residues processed: 359 average time/residue: 0.3155 time to fit residues: 168.3540 Evaluate side-chains 363 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 311 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 308 ASN E 318 HIS J 43 GLN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17835 Z= 0.247 Angle : 0.558 10.198 24256 Z= 0.282 Chirality : 0.044 0.255 2799 Planarity : 0.004 0.037 2985 Dihedral : 5.672 56.052 2822 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.93 % Allowed : 15.83 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.01 (0.18), residues: 2103 helix: 1.46 (0.21), residues: 595 sheet: -0.38 (0.20), residues: 619 loop : -0.61 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 319 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE A 221 TYR 0.023 0.001 TYR A 299 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 317 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7337 (mtt180) REVERT: A 224 GLN cc_start: 0.8403 (tt0) cc_final: 0.8033 (tt0) REVERT: A 323 PHE cc_start: 0.7097 (t80) cc_final: 0.6436 (t80) REVERT: B 24 ASP cc_start: 0.7016 (t0) cc_final: 0.6772 (p0) REVERT: B 112 MET cc_start: 0.8098 (tpp) cc_final: 0.7889 (tpp) REVERT: B 204 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7853 (mm110) REVERT: B 209 GLU cc_start: 0.7778 (tt0) cc_final: 0.7361 (tt0) REVERT: C 283 MET cc_start: 0.7272 (mmp) cc_final: 0.7067 (tpt) REVERT: D 15 PHE cc_start: 0.8533 (m-80) cc_final: 0.8138 (m-80) REVERT: D 21 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6902 (ttp-110) REVERT: D 93 LYS cc_start: 0.8481 (tptp) cc_final: 0.8045 (mmmm) REVERT: D 156 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8283 (mtmt) REVERT: D 164 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7613 (mtp-110) REVERT: D 261 THR cc_start: 0.8481 (m) cc_final: 0.8085 (t) REVERT: D 264 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7883 (mm) REVERT: D 310 PHE cc_start: 0.8343 (m-10) cc_final: 0.8103 (m-10) REVERT: E 98 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8458 (mt) REVERT: E 178 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7577 (mt-10) REVERT: E 276 MET cc_start: 0.8663 (tpp) cc_final: 0.8398 (mmm) REVERT: E 296 MET cc_start: 0.7245 (ttp) cc_final: 0.6924 (ttp) REVERT: E 301 SER cc_start: 0.8976 (m) cc_final: 0.8573 (m) REVERT: E 305 ILE cc_start: 0.8455 (mm) cc_final: 0.8053 (mm) REVERT: E 337 ILE cc_start: 0.8719 (tp) cc_final: 0.8420 (tp) REVERT: E 356 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.5006 (t80) REVERT: I 13 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4385 (ppp) REVERT: I 90 GLN cc_start: 0.9286 (pp30) cc_final: 0.9075 (pp30) REVERT: J 112 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8615 (t) REVERT: L 79 GLN cc_start: 0.7618 (mp10) cc_final: 0.7336 (mp10) REVERT: K 5 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7774 (mm-40) REVERT: K 102 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8389 (mmm-85) REVERT: K 105 MET cc_start: 0.8625 (mtm) cc_final: 0.7983 (mtt) outliers start: 74 outliers final: 53 residues processed: 356 average time/residue: 0.3030 time to fit residues: 160.2939 Evaluate side-chains 373 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 315 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 308 ASN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 GLN E 318 HIS J 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17835 Z= 0.220 Angle : 0.546 9.514 24256 Z= 0.277 Chirality : 0.043 0.257 2799 Planarity : 0.004 0.037 2985 Dihedral : 5.611 56.407 2822 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.72 % Allowed : 16.46 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2103 helix: 1.50 (0.21), residues: 595 sheet: -0.27 (0.20), residues: 603 loop : -0.64 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 103 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE A 221 TYR 0.023 0.001 TYR A 299 ARG 0.007 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 314 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7337 (mtt180) REVERT: A 224 GLN cc_start: 0.8416 (tt0) cc_final: 0.8028 (tt0) REVERT: A 323 PHE cc_start: 0.7156 (t80) cc_final: 0.6452 (t80) REVERT: B 17 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7821 (mtt-85) REVERT: B 24 ASP cc_start: 0.7003 (t0) cc_final: 0.6775 (p0) REVERT: B 112 MET cc_start: 0.8108 (tpp) cc_final: 0.7894 (tpp) REVERT: B 258 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7205 (t80) REVERT: C 141 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7847 (mtt90) REVERT: C 283 MET cc_start: 0.7257 (mmp) cc_final: 0.7056 (tpt) REVERT: D 15 PHE cc_start: 0.8533 (m-80) cc_final: 0.8098 (m-80) REVERT: D 21 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6903 (ttp-110) REVERT: D 93 LYS cc_start: 0.8471 (tptp) cc_final: 0.7939 (mmmm) REVERT: D 156 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8280 (mtmt) REVERT: D 261 THR cc_start: 0.8469 (m) cc_final: 0.8022 (t) REVERT: D 264 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7894 (mm) REVERT: D 310 PHE cc_start: 0.8328 (m-10) cc_final: 0.8099 (m-10) REVERT: E 98 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8468 (mt) REVERT: E 178 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7577 (mt-10) REVERT: E 296 MET cc_start: 0.7165 (ttp) cc_final: 0.6837 (ttp) REVERT: E 301 SER cc_start: 0.8982 (m) cc_final: 0.8535 (m) REVERT: E 305 ILE cc_start: 0.8432 (mm) cc_final: 0.8049 (mm) REVERT: E 337 ILE cc_start: 0.8730 (tp) cc_final: 0.8431 (tp) REVERT: E 356 TYR cc_start: 0.5409 (OUTLIER) cc_final: 0.5044 (t80) REVERT: I 13 MET cc_start: 0.4854 (OUTLIER) cc_final: 0.4440 (ppp) REVERT: I 90 GLN cc_start: 0.9273 (pp30) cc_final: 0.9063 (pp30) REVERT: J 112 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8622 (t) REVERT: L 79 GLN cc_start: 0.7653 (mp10) cc_final: 0.7382 (mp10) REVERT: K 5 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7716 (mm-40) REVERT: K 102 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8411 (mmm-85) REVERT: K 105 MET cc_start: 0.8626 (mtm) cc_final: 0.7987 (mtt) outliers start: 70 outliers final: 56 residues processed: 352 average time/residue: 0.3306 time to fit residues: 173.7037 Evaluate side-chains 372 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 310 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 175 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN B 308 ASN D 190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17835 Z= 0.389 Angle : 0.624 9.578 24256 Z= 0.316 Chirality : 0.046 0.254 2799 Planarity : 0.004 0.039 2985 Dihedral : 5.813 54.961 2822 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.98 % Allowed : 16.52 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.07 (0.18), residues: 2103 helix: 1.40 (0.21), residues: 595 sheet: -0.43 (0.20), residues: 605 loop : -0.66 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 183 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.002 PHE A 221 TYR 0.025 0.002 TYR A 299 ARG 0.008 0.001 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 327 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7408 (mtt180) REVERT: A 224 GLN cc_start: 0.8435 (tt0) cc_final: 0.8016 (tt0) REVERT: B 17 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7739 (mtt-85) REVERT: B 112 MET cc_start: 0.8185 (tpp) cc_final: 0.7938 (tpp) REVERT: C 338 TYR cc_start: 0.7918 (t80) cc_final: 0.7712 (t80) REVERT: D 15 PHE cc_start: 0.8579 (m-80) cc_final: 0.8172 (m-80) REVERT: D 21 ARG cc_start: 0.7130 (ttp-110) cc_final: 0.6548 (ttp-110) REVERT: D 93 LYS cc_start: 0.8506 (tptp) cc_final: 0.7888 (mmmm) REVERT: D 156 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8341 (mtmt) REVERT: D 261 THR cc_start: 0.8503 (m) cc_final: 0.8090 (t) REVERT: D 264 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8034 (mm) REVERT: E 98 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8576 (mt) REVERT: E 296 MET cc_start: 0.7208 (ttp) cc_final: 0.6793 (ttp) REVERT: E 301 SER cc_start: 0.8994 (m) cc_final: 0.8555 (m) REVERT: E 305 ILE cc_start: 0.8449 (mm) cc_final: 0.8086 (mm) REVERT: E 337 ILE cc_start: 0.8725 (tp) cc_final: 0.8464 (tp) REVERT: E 356 TYR cc_start: 0.5460 (OUTLIER) cc_final: 0.5063 (t80) REVERT: I 13 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4437 (ppp) REVERT: L 79 GLN cc_start: 0.7613 (mp10) cc_final: 0.7376 (mp10) REVERT: K 5 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7769 (mm-40) REVERT: K 102 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8490 (mmm-85) REVERT: K 105 MET cc_start: 0.8714 (mtm) cc_final: 0.8279 (mtt) outliers start: 75 outliers final: 61 residues processed: 371 average time/residue: 0.3104 time to fit residues: 168.9669 Evaluate side-chains 385 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 204 GLN B 308 ASN D 189 ASN D 190 GLN E 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17835 Z= 0.233 Angle : 0.584 9.536 24256 Z= 0.296 Chirality : 0.044 0.256 2799 Planarity : 0.004 0.037 2985 Dihedral : 5.706 56.314 2822 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.56 % Allowed : 16.99 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2103 helix: 1.50 (0.21), residues: 595 sheet: -0.33 (0.20), residues: 603 loop : -0.59 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 103 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.001 PHE A 221 TYR 0.025 0.001 TYR A 299 ARG 0.007 0.000 ARG C 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 321 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7365 (mtt180) REVERT: A 224 GLN cc_start: 0.8425 (tt0) cc_final: 0.8015 (tt0) REVERT: B 17 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7720 (mtt90) REVERT: B 112 MET cc_start: 0.8160 (tpp) cc_final: 0.7938 (tpp) REVERT: C 141 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7875 (mtt90) REVERT: C 338 TYR cc_start: 0.7896 (t80) cc_final: 0.7679 (t80) REVERT: D 15 PHE cc_start: 0.8542 (m-80) cc_final: 0.8154 (m-80) REVERT: D 93 LYS cc_start: 0.8480 (tptp) cc_final: 0.7937 (mmmm) REVERT: D 112 MET cc_start: 0.8253 (tpp) cc_final: 0.7797 (tpp) REVERT: D 156 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8341 (mtmt) REVERT: D 261 THR cc_start: 0.8488 (m) cc_final: 0.8048 (t) REVERT: E 98 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8461 (mt) REVERT: E 178 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7490 (mt-10) REVERT: E 296 MET cc_start: 0.7132 (ttp) cc_final: 0.6731 (ttp) REVERT: E 301 SER cc_start: 0.9004 (m) cc_final: 0.8580 (m) REVERT: E 305 ILE cc_start: 0.8439 (mm) cc_final: 0.8086 (mm) REVERT: E 337 ILE cc_start: 0.8744 (tp) cc_final: 0.8475 (tp) REVERT: E 356 TYR cc_start: 0.5443 (OUTLIER) cc_final: 0.5077 (t80) REVERT: I 13 MET cc_start: 0.4939 (OUTLIER) cc_final: 0.4644 (ppp) REVERT: L 79 GLN cc_start: 0.7618 (mp10) cc_final: 0.7349 (mp10) REVERT: K 5 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7795 (mm-40) REVERT: K 102 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8509 (mmm-85) REVERT: K 105 MET cc_start: 0.8658 (mtm) cc_final: 0.8201 (mtt) outliers start: 67 outliers final: 59 residues processed: 359 average time/residue: 0.3132 time to fit residues: 167.0802 Evaluate side-chains 374 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 312 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 0.0030 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 190 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN D 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102669 restraints weight = 21214.670| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.69 r_work: 0.2862 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 17835 Z= 0.258 Angle : 0.761 59.200 24256 Z= 0.429 Chirality : 0.045 0.473 2799 Planarity : 0.004 0.037 2985 Dihedral : 5.758 56.334 2822 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.40 % Allowed : 17.26 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.07 (0.18), residues: 2103 helix: 1.52 (0.21), residues: 595 sheet: -0.33 (0.20), residues: 603 loop : -0.59 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 103 HIS 0.027 0.001 HIS B 142 PHE 0.014 0.001 PHE A 221 TYR 0.024 0.001 TYR A 299 ARG 0.006 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.09 seconds wall clock time: 76 minutes 44.17 seconds (4604.17 seconds total)