Starting phenix.real_space_refine on Wed Jul 30 23:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xw5_33491/07_2025/7xw5_33491_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw5_33491/07_2025/7xw5_33491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xw5_33491/07_2025/7xw5_33491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw5_33491/07_2025/7xw5_33491.map" model { file = "/net/cci-nas-00/data/ceres_data/7xw5_33491/07_2025/7xw5_33491_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw5_33491/07_2025/7xw5_33491_neut.cif" } resolution = 2.96 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= -0.002 sd= 0.093 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 95 5.16 5 C 8177 2.51 5 N 2059 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12618 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1964 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4517 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 545} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "X" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 670 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "Y" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 838 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "R" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 577 Unusual residues: {'CLR': 14, 'HOI': 1, 'NAG': 4, 'PLM': 5} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" 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: "Y" 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 Time building chain proxies: 7.69, per 1000 atoms: 0.61 Number of scatterers: 12618 At special positions: 0 Unit cell: (80.325, 101.745, 192.78, 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 95 16.00 O 2287 8.00 N 2059 7.00 C 8177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 31 " - pdb=" SG CYS R 41 " distance=2.04 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.05 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.04 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.03 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.05 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.02 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 36 " - pdb=" SG CYS Y 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 39 " - pdb=" SG CYS Y 125 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 47 " - pdb=" SG CYS Y 103 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 51 " - pdb=" SG CYS Y 105 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 108 " - pdb=" SG CYS Y 115 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 801 " - " ASN R 198 " " NAG R 802 " - " ASN R 177 " " NAG R 803 " - " ASN R 99 " " NAG R 804 " - " ASN R 77 " " NAG X 201 " - " ASN X 78 " " NAG X 202 " - " ASN X 52 " " NAG Y 201 " - " ASN Y 43 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.7 seconds 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2890 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 31.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.705A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.111A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.676A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.765A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 265 through 270 removed outlier: 4.070A pdb=" N LEU R 270 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 286 removed outlier: 3.536A pdb=" N HIS R 282 " --> pdb=" O TYR R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 389 Processing helix chain 'R' and resid 414 through 442 removed outlier: 4.421A pdb=" N TRP R 422 " --> pdb=" O ARG R 418 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 423 " --> pdb=" O ILE R 419 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 432 " --> pdb=" O ALA R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 447 through 478 Processing helix chain 'R' and resid 480 through 483 Processing helix chain 'R' and resid 484 through 491 Processing helix chain 'R' and resid 491 through 525 removed outlier: 3.789A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 528 through 532 removed outlier: 3.582A pdb=" N LYS R 532 " --> pdb=" O LEU R 529 " (cutoff:3.500A) Processing helix chain 'R' and resid 534 through 559 removed outlier: 3.500A pdb=" N ALA R 538 " --> pdb=" O ARG R 534 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS R 548 " --> pdb=" O GLY R 544 " (cutoff:3.500A) Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 576 through 609 removed outlier: 3.630A pdb=" N PHE R 594 " --> pdb=" O ASN R 590 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 649 removed outlier: 3.757A pdb=" N ALA R 623 " --> pdb=" O ASP R 619 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 628 " --> pdb=" O LYS R 624 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU R 629 " --> pdb=" O ARG R 625 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS R 636 " --> pdb=" O THR R 632 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 666 removed outlier: 3.545A pdb=" N LYS R 660 " --> pdb=" O VAL R 656 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 668 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 682 through 695 Processing helix chain 'X' and resid 40 through 45 removed outlier: 3.753A pdb=" N LYS X 45 " --> pdb=" O LEU X 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.373A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.712A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.596A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.756A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.830A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.960A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.656A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.697A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.991A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 33 through 35 removed outlier: 3.764A pdb=" N ILE R 85 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE R 154 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS R 183 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU R 156 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU R 180 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL R 205 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU R 182 " --> pdb=" O VAL R 205 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP R 203 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA R 275 " --> pdb=" O THR R 399 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AB4, first strand: chain 'R' and resid 97 through 98 removed outlier: 4.137A pdb=" N LYS R 123 " --> pdb=" O PHE R 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 166 through 167 Processing sheet with id=AB6, first strand: chain 'X' and resid 11 through 14 removed outlier: 4.267A pdb=" N CYS X 28 " --> pdb=" O ASP Y 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 53 through 55 removed outlier: 7.007A pdb=" N VAL X 53 " --> pdb=" O ASP Y 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'X' and resid 59 through 70 removed outlier: 6.336A pdb=" N ALA X 81 " --> pdb=" O LYS X 63 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR X 65 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS X 79 " --> pdb=" O TYR X 65 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG X 67 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU X 77 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR X 69 " --> pdb=" O LYS X 75 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS X 75 " --> pdb=" O THR X 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 91 through 92 Processing sheet with id=AC1, first strand: chain 'Y' and resid 23 through 31 Processing sheet with id=AC2, first strand: chain 'Y' and resid 71 through 83 removed outlier: 6.153A pdb=" N SER Y 102 " --> pdb=" O ARG Y 75 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE Y 77 " --> pdb=" O ALA Y 100 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA Y 100 " --> pdb=" O PHE Y 77 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR Y 79 " --> pdb=" O PRO Y 98 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR Y 81 " --> pdb=" O SER Y 96 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER Y 96 " --> pdb=" O THR Y 81 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU Y 83 " --> pdb=" O TYR Y 94 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR Y 94 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1356 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: 3.91 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1960 1.27 - 1.41: 3186 1.41 - 1.55: 7380 1.55 - 1.69: 264 1.69 - 1.83: 126 Bond restraints: 12916 Sorted by residual: bond pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 1.520 1.339 0.182 1.31e-02 5.83e+03 1.92e+02 bond pdb=" CA ALA B 104 " pdb=" CB ALA B 104 " ideal model delta sigma weight residual 1.535 1.403 0.132 1.32e-02 5.74e+03 1.00e+02 bond pdb=" CA PHE B 292 " pdb=" C PHE B 292 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.33e-02 5.65e+03 9.00e+01 bond pdb=" C ALA B 104 " pdb=" O ALA B 104 " ideal model delta sigma weight residual 1.235 1.128 0.107 1.14e-02 7.69e+03 8.84e+01 bond pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 1.526 1.416 0.109 1.25e-02 6.40e+03 7.67e+01 ... (remaining 12911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 16376 3.44 - 6.89: 1171 6.89 - 10.33: 19 10.33 - 13.77: 1 13.77 - 17.22: 1 Bond angle restraints: 17568 Sorted by residual: angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 108.46 91.24 17.22 1.51e+00 4.39e-01 1.30e+02 angle pdb=" N PHE B 292 " pdb=" CA PHE B 292 " pdb=" C PHE B 292 " ideal model delta sigma weight residual 113.56 122.99 -9.43 1.39e+00 5.18e-01 4.60e+01 angle pdb=" C TYR B 105 " pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " ideal model delta sigma weight residual 109.72 98.98 10.74 1.61e+00 3.86e-01 4.45e+01 angle pdb=" CA ASP N 50 " pdb=" CB ASP N 50 " pdb=" CG ASP N 50 " ideal model delta sigma weight residual 112.60 119.01 -6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" N LYS A 25 " pdb=" CA LYS A 25 " pdb=" C LYS A 25 " ideal model delta sigma weight residual 111.14 104.30 6.84 1.08e+00 8.57e-01 4.01e+01 ... (remaining 17563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 8192 23.95 - 47.91: 312 47.91 - 71.86: 32 71.86 - 95.82: 13 95.82 - 119.77: 1 Dihedral angle restraints: 8550 sinusoidal: 4084 harmonic: 4466 Sorted by residual: dihedral pdb=" C TYR B 105 " pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " ideal model delta harmonic sigma weight residual -122.60 -100.77 -21.83 0 2.50e+00 1.60e-01 7.62e+01 dihedral pdb=" CB CYS X 10 " pdb=" SG CYS X 10 " pdb=" SG CYS X 60 " pdb=" CB CYS X 60 " ideal model delta sinusoidal sigma weight residual 93.00 166.18 -73.18 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CB CYS R 284 " pdb=" SG CYS R 284 " pdb=" SG CYS R 408 " pdb=" CB CYS R 408 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 8547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 1875 0.177 - 0.354: 156 0.354 - 0.531: 7 0.531 - 0.707: 0 0.707 - 0.884: 1 Chirality restraints: 2039 Sorted by residual: chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2036 not shown) Planarity restraints: 2139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HOI R 805 " 0.048 2.00e-02 2.50e+03 1.40e-01 4.42e+02 pdb=" C11 HOI R 805 " -0.000 2.00e-02 2.50e+03 pdb=" C12 HOI R 805 " 0.119 2.00e-02 2.50e+03 pdb=" C13 HOI R 805 " 0.167 2.00e-02 2.50e+03 pdb=" C14 HOI R 805 " 0.029 2.00e-02 2.50e+03 pdb=" C15 HOI R 805 " 0.003 2.00e-02 2.50e+03 pdb=" C16 HOI R 805 " -0.208 2.00e-02 2.50e+03 pdb=" C9 HOI R 805 " 0.116 2.00e-02 2.50e+03 pdb=" O5 HOI R 805 " -0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 348 " -0.236 2.00e-02 2.50e+03 1.28e-01 3.29e+02 pdb=" CG TYR A 348 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR A 348 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 TYR A 348 " 0.102 2.00e-02 2.50e+03 pdb=" CE1 TYR A 348 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR A 348 " 0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 348 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 348 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.178 2.00e-02 2.50e+03 9.20e-02 2.12e+02 pdb=" CG TRP B 99 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.088 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.121 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.117 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.095 2.00e-02 2.50e+03 ... (remaining 2136 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 96 2.68 - 3.23: 11480 3.23 - 3.79: 18906 3.79 - 4.34: 27076 4.34 - 4.90: 43925 Nonbonded interactions: 101483 Sorted by model distance: nonbonded pdb=" N TYR B 105 " pdb=" O TYR B 105 " model vdw 2.119 2.496 nonbonded pdb=" O TRP B 339 " pdb=" OD1 ASN B 340 " model vdw 2.197 3.040 nonbonded pdb=" CG2 THR A 40 " pdb=" OD1 ASN A 218 " model vdw 2.461 3.460 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.539 3.040 nonbonded pdb=" OE2 GLU R 506 " pdb=" CG1 VAL R 586 " model vdw 2.539 3.460 ... (remaining 101478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.014 0.182 12940 Z= 0.838 Angle : 1.880 17.215 17623 Z= 1.232 Chirality : 0.105 0.884 2039 Planarity : 0.016 0.166 2132 Dihedral : 12.541 119.769 5609 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.53 % Allowed : 4.53 % Favored : 94.94 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.98 (0.20), residues: 1502 helix: -0.91 (0.21), residues: 404 sheet: -0.47 (0.30), residues: 280 loop : -0.45 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.178 0.031 TRP B 99 HIS 0.017 0.004 HIS A 347 PHE 0.067 0.016 PHE R 269 TYR 0.236 0.019 TYR A 348 ARG 0.010 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01380 ( 7) link_NAG-ASN : angle 4.23946 ( 21) hydrogen bonds : bond 0.17916 ( 491) hydrogen bonds : angle 7.15498 ( 1356) SS BOND : bond 0.00919 ( 17) SS BOND : angle 1.98139 ( 34) covalent geometry : bond 0.01389 (12916) covalent geometry : angle 1.87531 (17568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 269 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6749 (mm110) REVERT: A 35 GLN cc_start: 0.7711 (tt0) cc_final: 0.7058 (mm-40) REVERT: A 58 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7514 (ttpp) REVERT: A 236 GLN cc_start: 0.8410 (mt0) cc_final: 0.8196 (pt0) REVERT: A 346 ARG cc_start: 0.6783 (mtp180) cc_final: 0.6484 (mtm-85) REVERT: B 57 LYS cc_start: 0.8541 (pttm) cc_final: 0.8295 (pttt) REVERT: B 263 THR cc_start: 0.8521 (t) cc_final: 0.8255 (m) REVERT: B 303 ASP cc_start: 0.6724 (t0) cc_final: 0.6244 (m-30) REVERT: N 83 MET cc_start: 0.6648 (ttm) cc_final: 0.6444 (ttp) REVERT: R 32 HIS cc_start: 0.7084 (m90) cc_final: 0.6860 (m-70) REVERT: R 57 LEU cc_start: 0.8659 (mp) cc_final: 0.8331 (tp) REVERT: R 140 MET cc_start: 0.7151 (ptm) cc_final: 0.6780 (ptm) REVERT: R 191 SER cc_start: 0.8897 (t) cc_final: 0.8667 (p) REVERT: R 248 HIS cc_start: 0.6975 (m-70) cc_final: 0.6566 (m-70) REVERT: R 434 PHE cc_start: 0.8063 (t80) cc_final: 0.7791 (t80) REVERT: R 539 CYS cc_start: 0.7962 (t) cc_final: 0.7615 (m) REVERT: R 610 ASN cc_start: 0.7001 (p0) cc_final: 0.6777 (p0) REVERT: R 651 LYS cc_start: 0.7064 (mttt) cc_final: 0.6819 (tppt) REVERT: R 683 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7346 (pttt) REVERT: X 44 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.7005 (mttp) REVERT: X 91 LYS cc_start: 0.7539 (mttp) cc_final: 0.7211 (mtmt) REVERT: Y 52 MET cc_start: 0.7878 (tpp) cc_final: 0.7280 (tmm) outliers start: 7 outliers final: 2 residues processed: 274 average time/residue: 1.0832 time to fit residues: 327.9378 Evaluate side-chains 168 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain X residue 44 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 13 GLN R 33 GLN R 170 ASN R 484 HIS Y 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.203802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140150 restraints weight = 14520.895| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.73 r_work: 0.3412 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12940 Z= 0.154 Angle : 0.693 9.653 17623 Z= 0.358 Chirality : 0.045 0.216 2039 Planarity : 0.005 0.056 2132 Dihedral : 7.679 59.149 2820 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.00 % Allowed : 12.08 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.17 (0.21), residues: 1502 helix: 1.17 (0.24), residues: 413 sheet: -0.44 (0.28), residues: 329 loop : -0.11 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 297 HIS 0.008 0.001 HIS A 347 PHE 0.023 0.002 PHE R 434 TYR 0.015 0.001 TYR R 667 ARG 0.005 0.001 ARG A 370 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 7) link_NAG-ASN : angle 2.52556 ( 21) hydrogen bonds : bond 0.04822 ( 491) hydrogen bonds : angle 5.10438 ( 1356) SS BOND : bond 0.00332 ( 17) SS BOND : angle 1.33179 ( 34) covalent geometry : bond 0.00356 (12916) covalent geometry : angle 0.68586 (17568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6841 (mm-40) cc_final: 0.6569 (mm110) REVERT: A 35 GLN cc_start: 0.8056 (tt0) cc_final: 0.7233 (mm-40) REVERT: A 59 GLN cc_start: 0.7983 (tp40) cc_final: 0.7582 (mm110) REVERT: A 239 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8032 (p0) REVERT: A 289 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 301 TYR cc_start: 0.7991 (m-80) cc_final: 0.7729 (m-80) REVERT: A 346 ARG cc_start: 0.7209 (mtp180) cc_final: 0.6671 (mtm-85) REVERT: B 59 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: B 98 SER cc_start: 0.8705 (m) cc_final: 0.8441 (t) REVERT: B 155 ASN cc_start: 0.7523 (t0) cc_final: 0.7240 (m110) REVERT: B 170 ASP cc_start: 0.8476 (t0) cc_final: 0.8191 (t0) REVERT: B 226 GLU cc_start: 0.7074 (pt0) cc_final: 0.6846 (pt0) REVERT: B 263 THR cc_start: 0.8622 (t) cc_final: 0.8317 (m) REVERT: N 34 MET cc_start: 0.7743 (mmm) cc_final: 0.7047 (mmm) REVERT: N 83 MET cc_start: 0.6417 (ttm) cc_final: 0.5755 (ttm) REVERT: R 37 PHE cc_start: 0.7124 (m-80) cc_final: 0.6877 (m-80) REVERT: R 57 LEU cc_start: 0.8311 (mp) cc_final: 0.7810 (tp) REVERT: R 140 MET cc_start: 0.7225 (ptm) cc_final: 0.6933 (pmm) REVERT: R 153 PHE cc_start: 0.7636 (m-80) cc_final: 0.6815 (p90) REVERT: R 191 SER cc_start: 0.8800 (t) cc_final: 0.8572 (p) REVERT: R 271 HIS cc_start: 0.5937 (OUTLIER) cc_final: 0.5711 (m90) REVERT: R 534 ARG cc_start: 0.5924 (ttp80) cc_final: 0.5432 (mmm160) REVERT: R 610 ASN cc_start: 0.7195 (p0) cc_final: 0.6977 (p0) REVERT: R 651 LYS cc_start: 0.7045 (mttt) cc_final: 0.6520 (tppt) REVERT: X 15 ASN cc_start: 0.5862 (t0) cc_final: 0.5592 (p0) REVERT: X 47 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8071 (mpp) REVERT: X 91 LYS cc_start: 0.7494 (mttp) cc_final: 0.7182 (mtmt) REVERT: Y 25 THR cc_start: 0.6035 (m) cc_final: 0.5828 (m) REVERT: Y 70 ASP cc_start: 0.8525 (m-30) cc_final: 0.7981 (t0) REVERT: Y 75 ARG cc_start: 0.6916 (ttm-80) cc_final: 0.6564 (ttp80) REVERT: Y 76 ASP cc_start: 0.8130 (t0) cc_final: 0.7238 (p0) outliers start: 53 outliers final: 15 residues processed: 227 average time/residue: 0.9593 time to fit residues: 242.8465 Evaluate side-chains 176 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 276 ASP Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 115 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 31 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 33 optimal weight: 0.0030 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN N 3 GLN R 432 ASN Y 30 HIS ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.203782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147929 restraints weight = 14870.960| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.54 r_work: 0.3492 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12940 Z= 0.155 Angle : 0.646 10.117 17623 Z= 0.333 Chirality : 0.045 0.209 2039 Planarity : 0.004 0.047 2132 Dihedral : 7.309 59.291 2814 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.55 % Allowed : 15.63 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.33 (0.22), residues: 1502 helix: 1.56 (0.25), residues: 406 sheet: -0.45 (0.28), residues: 336 loop : -0.09 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 36 HIS 0.011 0.001 HIS X 83 PHE 0.014 0.002 PHE B 151 TYR 0.012 0.001 TYR A 348 ARG 0.005 0.000 ARG Y 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 7) link_NAG-ASN : angle 2.04462 ( 21) hydrogen bonds : bond 0.04636 ( 491) hydrogen bonds : angle 4.81244 ( 1356) SS BOND : bond 0.00367 ( 17) SS BOND : angle 1.43523 ( 34) covalent geometry : bond 0.00366 (12916) covalent geometry : angle 0.64046 (17568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8109 (tt0) cc_final: 0.7563 (mm-40) REVERT: A 54 SER cc_start: 0.8531 (m) cc_final: 0.7984 (p) REVERT: A 58 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7306 (tptt) REVERT: A 59 GLN cc_start: 0.8032 (tp40) cc_final: 0.7808 (mm110) REVERT: A 239 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 301 TYR cc_start: 0.8121 (m-80) cc_final: 0.7791 (m-80) REVERT: A 346 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6801 (mtm-85) REVERT: B 23 LYS cc_start: 0.9121 (tptp) cc_final: 0.8795 (mtmt) REVERT: B 59 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: B 263 THR cc_start: 0.8626 (t) cc_final: 0.8388 (m) REVERT: B 303 ASP cc_start: 0.7141 (t0) cc_final: 0.6838 (m-30) REVERT: G 51 LEU cc_start: 0.8333 (mt) cc_final: 0.7922 (mt) REVERT: N 34 MET cc_start: 0.7805 (mmm) cc_final: 0.7280 (mmm) REVERT: N 83 MET cc_start: 0.6339 (ttm) cc_final: 0.5651 (ttm) REVERT: R 37 PHE cc_start: 0.7218 (m-80) cc_final: 0.6930 (m-80) REVERT: R 57 LEU cc_start: 0.8503 (mp) cc_final: 0.8107 (tp) REVERT: R 403 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.7028 (t0) REVERT: R 432 ASN cc_start: 0.8275 (m-40) cc_final: 0.7806 (m110) REVERT: R 453 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6794 (tpt) REVERT: R 651 LYS cc_start: 0.7212 (mttt) cc_final: 0.6687 (tppt) REVERT: X 29 MET cc_start: 0.7338 (mmm) cc_final: 0.7091 (mmm) REVERT: X 41 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7687 (tp) REVERT: X 91 LYS cc_start: 0.7824 (mttp) cc_final: 0.7580 (mtmt) REVERT: Y 52 MET cc_start: 0.8148 (tpt) cc_final: 0.7198 (tmm) REVERT: Y 57 ASN cc_start: 0.7318 (m110) cc_final: 0.6952 (m110) REVERT: Y 70 ASP cc_start: 0.8549 (m-30) cc_final: 0.7991 (t0) REVERT: Y 97 TYR cc_start: 0.7381 (p90) cc_final: 0.6730 (p90) outliers start: 47 outliers final: 21 residues processed: 196 average time/residue: 0.9313 time to fit residues: 204.0099 Evaluate side-chains 179 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 30 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 133 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS X 50 GLN ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.202249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143980 restraints weight = 14630.080| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.64 r_work: 0.3470 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12940 Z= 0.181 Angle : 0.639 10.316 17623 Z= 0.327 Chirality : 0.045 0.210 2039 Planarity : 0.004 0.052 2132 Dihedral : 7.420 59.992 2814 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.53 % Allowed : 15.86 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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 (0.22), residues: 1502 helix: 1.66 (0.25), residues: 398 sheet: -0.42 (0.28), residues: 330 loop : -0.14 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 36 HIS 0.022 0.002 HIS Y 30 PHE 0.015 0.002 PHE R 416 TYR 0.014 0.002 TYR R 82 ARG 0.009 0.000 ARG Y 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 7) link_NAG-ASN : angle 1.83960 ( 21) hydrogen bonds : bond 0.04614 ( 491) hydrogen bonds : angle 4.74633 ( 1356) SS BOND : bond 0.00446 ( 17) SS BOND : angle 1.34110 ( 34) covalent geometry : bond 0.00441 (12916) covalent geometry : angle 0.63421 (17568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7350 (tp40) cc_final: 0.7135 (tp40) REVERT: A 35 GLN cc_start: 0.8122 (tt0) cc_final: 0.7637 (mm-40) REVERT: A 58 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7295 (tptt) REVERT: A 59 GLN cc_start: 0.8049 (tp40) cc_final: 0.7812 (mm110) REVERT: A 239 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8101 (t0) REVERT: A 301 TYR cc_start: 0.8220 (m-80) cc_final: 0.7923 (m-80) REVERT: A 346 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6785 (mtm-85) REVERT: B 23 LYS cc_start: 0.9141 (tptp) cc_final: 0.8816 (mtmt) REVERT: B 59 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: B 226 GLU cc_start: 0.7667 (pt0) cc_final: 0.7463 (pt0) REVERT: B 263 THR cc_start: 0.8670 (t) cc_final: 0.8396 (m) REVERT: B 303 ASP cc_start: 0.7196 (t0) cc_final: 0.6873 (m-30) REVERT: G 51 LEU cc_start: 0.8328 (mt) cc_final: 0.7856 (mt) REVERT: N 34 MET cc_start: 0.7900 (mmm) cc_final: 0.7518 (mmm) REVERT: N 83 MET cc_start: 0.6288 (ttm) cc_final: 0.5615 (ttm) REVERT: R 37 PHE cc_start: 0.7218 (m-80) cc_final: 0.6847 (m-80) REVERT: R 144 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8276 (mt) REVERT: R 153 PHE cc_start: 0.7642 (m-80) cc_final: 0.6837 (p90) REVERT: R 403 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7181 (t0) REVERT: R 432 ASN cc_start: 0.8313 (m-40) cc_final: 0.7884 (m110) REVERT: R 453 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6840 (tpt) REVERT: R 651 LYS cc_start: 0.7289 (mttt) cc_final: 0.6755 (tppt) REVERT: X 29 MET cc_start: 0.7288 (mmm) cc_final: 0.6873 (mmm) REVERT: X 41 LEU cc_start: 0.8067 (mt) cc_final: 0.7739 (tp) REVERT: X 44 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6985 (tppt) REVERT: X 45 LYS cc_start: 0.8355 (pttm) cc_final: 0.7998 (pmtt) REVERT: X 91 LYS cc_start: 0.7762 (mttp) cc_final: 0.7463 (mtmt) REVERT: Y 52 MET cc_start: 0.8138 (tpt) cc_final: 0.7028 (tmm) REVERT: Y 57 ASN cc_start: 0.7545 (m110) cc_final: 0.7141 (m110) REVERT: Y 70 ASP cc_start: 0.8548 (m-30) cc_final: 0.7927 (t0) outliers start: 60 outliers final: 31 residues processed: 195 average time/residue: 0.9398 time to fit residues: 204.5903 Evaluate side-chains 178 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 115 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS X 50 GLN ** X 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.203960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144348 restraints weight = 14537.696| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.74 r_work: 0.3449 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12940 Z= 0.125 Angle : 0.573 8.478 17623 Z= 0.293 Chirality : 0.043 0.211 2039 Planarity : 0.004 0.050 2132 Dihedral : 7.026 59.273 2814 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.15 % Allowed : 16.31 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.48 (0.22), residues: 1502 helix: 1.92 (0.26), residues: 399 sheet: -0.47 (0.28), residues: 336 loop : -0.08 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 36 HIS 0.008 0.001 HIS X 83 PHE 0.011 0.001 PHE R 416 TYR 0.013 0.001 TYR B 111 ARG 0.005 0.000 ARG Y 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 7) link_NAG-ASN : angle 1.67048 ( 21) hydrogen bonds : bond 0.04071 ( 491) hydrogen bonds : angle 4.54410 ( 1356) SS BOND : bond 0.00305 ( 17) SS BOND : angle 0.95990 ( 34) covalent geometry : bond 0.00293 (12916) covalent geometry : angle 0.56941 (17568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7432 (tp40) cc_final: 0.7153 (mm110) REVERT: A 35 GLN cc_start: 0.8198 (tt0) cc_final: 0.7576 (mm-40) REVERT: A 54 SER cc_start: 0.8485 (m) cc_final: 0.7949 (p) REVERT: A 58 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7082 (tptt) REVERT: A 59 GLN cc_start: 0.8080 (tp40) cc_final: 0.7748 (mm110) REVERT: A 301 TYR cc_start: 0.8220 (m-80) cc_final: 0.7925 (m-80) REVERT: A 346 ARG cc_start: 0.7275 (mtp180) cc_final: 0.6755 (mtm-85) REVERT: B 23 LYS cc_start: 0.9168 (tptp) cc_final: 0.8814 (mtmt) REVERT: B 59 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: B 263 THR cc_start: 0.8626 (t) cc_final: 0.8343 (m) REVERT: B 303 ASP cc_start: 0.7241 (t0) cc_final: 0.6821 (m-30) REVERT: G 51 LEU cc_start: 0.8248 (mt) cc_final: 0.7744 (mt) REVERT: N 34 MET cc_start: 0.7904 (mmm) cc_final: 0.7512 (mmm) REVERT: N 83 MET cc_start: 0.6390 (ttm) cc_final: 0.5699 (ttm) REVERT: R 37 PHE cc_start: 0.7192 (m-80) cc_final: 0.6798 (m-80) REVERT: R 144 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8231 (mt) REVERT: R 153 PHE cc_start: 0.7713 (m-80) cc_final: 0.6803 (p90) REVERT: R 397 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7774 (p) REVERT: R 432 ASN cc_start: 0.8313 (m-40) cc_final: 0.7873 (m110) REVERT: R 453 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7129 (mtp) REVERT: R 542 MET cc_start: 0.9034 (tpp) cc_final: 0.8817 (mmm) REVERT: R 651 LYS cc_start: 0.7230 (mttt) cc_final: 0.6664 (tppt) REVERT: X 29 MET cc_start: 0.7355 (mmm) cc_final: 0.6811 (mmm) REVERT: X 41 LEU cc_start: 0.8002 (mt) cc_final: 0.7666 (tm) REVERT: X 45 LYS cc_start: 0.8327 (pttm) cc_final: 0.7981 (pmtt) REVERT: X 47 MET cc_start: 0.8538 (mtt) cc_final: 0.8024 (mtt) REVERT: X 91 LYS cc_start: 0.7731 (mttp) cc_final: 0.7394 (mtmt) REVERT: Y 52 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7138 (tmm) REVERT: Y 57 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7359 (m110) REVERT: Y 70 ASP cc_start: 0.8519 (m-30) cc_final: 0.7891 (t0) REVERT: Y 78 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7789 (tt) REVERT: Y 99 VAL cc_start: 0.6686 (m) cc_final: 0.6399 (t) REVERT: Y 120 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7210 (pt) outliers start: 55 outliers final: 28 residues processed: 193 average time/residue: 1.0060 time to fit residues: 219.8707 Evaluate side-chains 181 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 276 ASP Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 580 LEU Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 57 ASN Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain Y residue 120 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS X 50 GLN ** Y 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.201148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143664 restraints weight = 14792.700| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.56 r_work: 0.3449 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12940 Z= 0.201 Angle : 0.635 10.828 17623 Z= 0.323 Chirality : 0.045 0.213 2039 Planarity : 0.004 0.054 2132 Dihedral : 7.284 59.578 2814 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.46 % Allowed : 16.62 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.24 (0.22), residues: 1502 helix: 1.64 (0.25), residues: 404 sheet: -0.44 (0.28), residues: 330 loop : -0.29 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS X 83 PHE 0.016 0.002 PHE N 108 TYR 0.017 0.002 TYR R 82 ARG 0.004 0.000 ARG Y 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 7) link_NAG-ASN : angle 1.65111 ( 21) hydrogen bonds : bond 0.04629 ( 491) hydrogen bonds : angle 4.70439 ( 1356) SS BOND : bond 0.00372 ( 17) SS BOND : angle 1.08537 ( 34) covalent geometry : bond 0.00489 (12916) covalent geometry : angle 0.63168 (17568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7473 (tp40) cc_final: 0.7211 (mm110) REVERT: A 35 GLN cc_start: 0.8140 (tt0) cc_final: 0.7685 (mm-40) REVERT: A 58 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7277 (tptt) REVERT: A 59 GLN cc_start: 0.8060 (tp40) cc_final: 0.7784 (mm110) REVERT: A 301 TYR cc_start: 0.8315 (m-80) cc_final: 0.8078 (m-80) REVERT: A 346 ARG cc_start: 0.7301 (mtp180) cc_final: 0.6852 (mtm-85) REVERT: B 23 LYS cc_start: 0.9177 (tptp) cc_final: 0.8827 (mtmt) REVERT: B 59 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 263 THR cc_start: 0.8724 (t) cc_final: 0.8382 (m) REVERT: B 303 ASP cc_start: 0.7358 (t0) cc_final: 0.7063 (m-30) REVERT: G 51 LEU cc_start: 0.8436 (mt) cc_final: 0.7935 (mt) REVERT: N 34 MET cc_start: 0.7875 (mmm) cc_final: 0.7582 (mmm) REVERT: N 83 MET cc_start: 0.6325 (ttm) cc_final: 0.5505 (ttm) REVERT: R 144 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8119 (mt) REVERT: R 153 PHE cc_start: 0.7652 (m-80) cc_final: 0.6834 (p90) REVERT: R 403 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7244 (t0) REVERT: R 432 ASN cc_start: 0.8288 (m-40) cc_final: 0.7892 (m110) REVERT: R 453 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6921 (tpt) REVERT: R 535 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8720 (tt) REVERT: R 651 LYS cc_start: 0.7226 (mttt) cc_final: 0.6773 (tppt) REVERT: R 677 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8564 (mp) REVERT: X 29 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6886 (mmm) REVERT: X 44 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7135 (tppt) REVERT: X 47 MET cc_start: 0.8735 (mtt) cc_final: 0.8267 (mtt) REVERT: X 91 LYS cc_start: 0.8107 (mttp) cc_final: 0.7751 (mtmt) REVERT: Y 52 MET cc_start: 0.8201 (tpt) cc_final: 0.7167 (tmm) REVERT: Y 57 ASN cc_start: 0.7640 (m110) cc_final: 0.7329 (m110) REVERT: Y 120 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7221 (pt) outliers start: 59 outliers final: 36 residues processed: 188 average time/residue: 0.8525 time to fit residues: 181.2272 Evaluate side-chains 186 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 535 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 580 LEU Chi-restraints excluded: chain R residue 677 LEU Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 115 CYS Chi-restraints excluded: chain Y residue 120 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 70 HIS R 271 HIS X 83 HIS Y 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.202971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145714 restraints weight = 14523.539| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.52 r_work: 0.3477 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12940 Z= 0.127 Angle : 0.572 8.871 17623 Z= 0.292 Chirality : 0.043 0.210 2039 Planarity : 0.004 0.051 2132 Dihedral : 6.871 59.272 2814 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.70 % Allowed : 17.90 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.37 (0.22), residues: 1502 helix: 1.84 (0.26), residues: 406 sheet: -0.42 (0.28), residues: 336 loop : -0.24 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS X 83 PHE 0.011 0.001 PHE N 108 TYR 0.015 0.001 TYR R 82 ARG 0.004 0.000 ARG Y 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 7) link_NAG-ASN : angle 1.54341 ( 21) hydrogen bonds : bond 0.04039 ( 491) hydrogen bonds : angle 4.50727 ( 1356) SS BOND : bond 0.00288 ( 17) SS BOND : angle 0.92316 ( 34) covalent geometry : bond 0.00297 (12916) covalent geometry : angle 0.56899 (17568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7382 (tp40) cc_final: 0.7051 (mm110) REVERT: A 35 GLN cc_start: 0.8092 (tt0) cc_final: 0.7635 (mm-40) REVERT: A 58 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7233 (tptt) REVERT: A 59 GLN cc_start: 0.7975 (tp40) cc_final: 0.7751 (mm110) REVERT: A 301 TYR cc_start: 0.8315 (m-80) cc_final: 0.8018 (m-80) REVERT: A 346 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6772 (mtm-85) REVERT: A 368 ASP cc_start: 0.7949 (m-30) cc_final: 0.7532 (m-30) REVERT: B 23 LYS cc_start: 0.9189 (tptp) cc_final: 0.8855 (mtmt) REVERT: B 59 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: B 226 GLU cc_start: 0.7432 (pt0) cc_final: 0.7143 (pt0) REVERT: B 263 THR cc_start: 0.8645 (t) cc_final: 0.8368 (m) REVERT: B 303 ASP cc_start: 0.7229 (t0) cc_final: 0.6878 (m-30) REVERT: G 51 LEU cc_start: 0.8454 (mt) cc_final: 0.7969 (mt) REVERT: N 34 MET cc_start: 0.7845 (mmm) cc_final: 0.7554 (mmm) REVERT: N 83 MET cc_start: 0.6301 (ttm) cc_final: 0.5513 (ttm) REVERT: R 432 ASN cc_start: 0.8283 (m-40) cc_final: 0.7857 (m110) REVERT: R 453 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7094 (mtp) REVERT: R 534 ARG cc_start: 0.6019 (ttp80) cc_final: 0.5688 (mtp85) REVERT: R 651 LYS cc_start: 0.7231 (mttt) cc_final: 0.6758 (tppt) REVERT: X 29 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7053 (mmm) REVERT: X 45 LYS cc_start: 0.8341 (pttm) cc_final: 0.7935 (pmtt) REVERT: X 47 MET cc_start: 0.8702 (mtt) cc_final: 0.8282 (mtt) REVERT: X 91 LYS cc_start: 0.7922 (mttp) cc_final: 0.7586 (mtmt) REVERT: Y 52 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7077 (tmm) REVERT: Y 70 ASP cc_start: 0.8348 (m-30) cc_final: 0.7787 (t0) REVERT: Y 78 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7594 (tt) REVERT: Y 120 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7185 (pt) outliers start: 49 outliers final: 26 residues processed: 176 average time/residue: 0.8916 time to fit residues: 176.8912 Evaluate side-chains 170 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 91 GLN Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain Y residue 120 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 248 HIS R 271 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.201945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141946 restraints weight = 14619.849| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.72 r_work: 0.3445 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12940 Z= 0.161 Angle : 0.612 9.677 17623 Z= 0.309 Chirality : 0.044 0.206 2039 Planarity : 0.004 0.053 2132 Dihedral : 6.960 58.135 2814 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.55 % Allowed : 18.13 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.29 (0.22), residues: 1502 helix: 1.83 (0.26), residues: 404 sheet: -0.50 (0.27), residues: 343 loop : -0.30 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS R 105 PHE 0.014 0.001 PHE A 208 TYR 0.015 0.001 TYR R 82 ARG 0.003 0.000 ARG Y 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 7) link_NAG-ASN : angle 1.51350 ( 21) hydrogen bonds : bond 0.04300 ( 491) hydrogen bonds : angle 4.56637 ( 1356) SS BOND : bond 0.00318 ( 17) SS BOND : angle 0.98270 ( 34) covalent geometry : bond 0.00388 (12916) covalent geometry : angle 0.60931 (17568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7434 (tp40) cc_final: 0.7176 (mm110) REVERT: A 35 GLN cc_start: 0.8152 (tt0) cc_final: 0.7595 (mm-40) REVERT: A 58 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7206 (tptt) REVERT: A 59 GLN cc_start: 0.7973 (tp40) cc_final: 0.7685 (mm110) REVERT: A 301 TYR cc_start: 0.8309 (m-80) cc_final: 0.8046 (m-80) REVERT: A 346 ARG cc_start: 0.7195 (mtp180) cc_final: 0.6732 (mtm-85) REVERT: B 23 LYS cc_start: 0.9191 (tptp) cc_final: 0.8817 (mtmt) REVERT: B 59 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: B 226 GLU cc_start: 0.7293 (pt0) cc_final: 0.7054 (pt0) REVERT: B 263 THR cc_start: 0.8671 (t) cc_final: 0.8370 (m) REVERT: B 303 ASP cc_start: 0.7277 (t0) cc_final: 0.6830 (m-30) REVERT: G 51 LEU cc_start: 0.8434 (mt) cc_final: 0.7953 (mt) REVERT: N 34 MET cc_start: 0.7827 (mmm) cc_final: 0.7503 (mmm) REVERT: N 83 MET cc_start: 0.6191 (ttm) cc_final: 0.5405 (ttm) REVERT: R 144 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8169 (mt) REVERT: R 153 PHE cc_start: 0.7614 (m-80) cc_final: 0.6789 (p90) REVERT: R 173 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: R 403 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7241 (t0) REVERT: R 432 ASN cc_start: 0.8311 (m-40) cc_final: 0.7925 (m110) REVERT: R 453 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6733 (tpt) REVERT: R 651 LYS cc_start: 0.7235 (mttt) cc_final: 0.6767 (tppt) REVERT: R 677 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8546 (mp) REVERT: X 29 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6673 (mmm) REVERT: X 47 MET cc_start: 0.8805 (mtt) cc_final: 0.8383 (mtt) REVERT: X 91 LYS cc_start: 0.7948 (mttp) cc_final: 0.7557 (mtmt) REVERT: Y 52 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7508 (tmm) REVERT: Y 70 ASP cc_start: 0.8356 (m-30) cc_final: 0.7746 (t0) REVERT: Y 120 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7203 (pt) outliers start: 47 outliers final: 30 residues processed: 170 average time/residue: 0.8731 time to fit residues: 167.5017 Evaluate side-chains 173 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 173 GLN Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 580 LEU Chi-restraints excluded: chain R residue 677 LEU Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 120 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN R 248 HIS R 271 HIS ** X 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.202753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144455 restraints weight = 14606.768| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.58 r_work: 0.3467 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12940 Z= 0.135 Angle : 0.587 10.730 17623 Z= 0.297 Chirality : 0.043 0.197 2039 Planarity : 0.004 0.052 2132 Dihedral : 6.754 59.737 2814 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.25 % Allowed : 18.81 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.40 (0.22), residues: 1502 helix: 2.00 (0.26), residues: 404 sheet: -0.49 (0.27), residues: 343 loop : -0.26 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.005 0.001 HIS R 282 PHE 0.017 0.001 PHE A 208 TYR 0.015 0.001 TYR R 82 ARG 0.003 0.000 ARG Y 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 7) link_NAG-ASN : angle 1.41279 ( 21) hydrogen bonds : bond 0.04010 ( 491) hydrogen bonds : angle 4.44497 ( 1356) SS BOND : bond 0.00293 ( 17) SS BOND : angle 1.10365 ( 34) covalent geometry : bond 0.00322 (12916) covalent geometry : angle 0.58350 (17568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7453 (tp40) cc_final: 0.7124 (mm110) REVERT: A 35 GLN cc_start: 0.8125 (tt0) cc_final: 0.7652 (mm-40) REVERT: A 58 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7220 (tptt) REVERT: A 255 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.6807 (ptm160) REVERT: A 301 TYR cc_start: 0.8360 (m-80) cc_final: 0.8109 (m-80) REVERT: A 346 ARG cc_start: 0.7120 (mtp180) cc_final: 0.6722 (mtm-85) REVERT: B 23 LYS cc_start: 0.9256 (tptp) cc_final: 0.8917 (mtmt) REVERT: B 59 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: B 226 GLU cc_start: 0.7271 (pt0) cc_final: 0.7037 (pt0) REVERT: B 263 THR cc_start: 0.8634 (t) cc_final: 0.8343 (m) REVERT: B 303 ASP cc_start: 0.7273 (t0) cc_final: 0.6886 (m-30) REVERT: G 51 LEU cc_start: 0.8540 (mt) cc_final: 0.8105 (mt) REVERT: N 34 MET cc_start: 0.7866 (mmm) cc_final: 0.7527 (mmm) REVERT: N 83 MET cc_start: 0.6279 (ttm) cc_final: 0.5504 (ttm) REVERT: R 153 PHE cc_start: 0.7555 (m-80) cc_final: 0.6819 (p90) REVERT: R 403 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7203 (t0) REVERT: R 432 ASN cc_start: 0.8325 (m-40) cc_final: 0.7965 (m110) REVERT: R 453 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6907 (tpt) REVERT: R 534 ARG cc_start: 0.6028 (ttp80) cc_final: 0.5735 (mtp85) REVERT: R 651 LYS cc_start: 0.7318 (mttt) cc_final: 0.6821 (tppt) REVERT: R 677 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8493 (mp) REVERT: X 29 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6825 (mmm) REVERT: X 45 LYS cc_start: 0.8387 (pttm) cc_final: 0.8137 (pmtt) REVERT: X 91 LYS cc_start: 0.7750 (mttp) cc_final: 0.7413 (mtmt) REVERT: Y 33 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.7216 (mmm-85) REVERT: Y 52 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7347 (tmm) REVERT: Y 70 ASP cc_start: 0.8265 (m-30) cc_final: 0.7617 (t0) REVERT: Y 120 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7274 (pt) outliers start: 43 outliers final: 26 residues processed: 171 average time/residue: 0.9130 time to fit residues: 175.4356 Evaluate side-chains 172 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 677 LEU Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 220 HIS R 248 HIS R 271 HIS ** X 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.201625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143675 restraints weight = 14545.390| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.67 r_work: 0.3433 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12940 Z= 0.172 Angle : 0.631 12.067 17623 Z= 0.317 Chirality : 0.044 0.199 2039 Planarity : 0.004 0.053 2132 Dihedral : 6.948 59.257 2814 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.17 % Allowed : 18.88 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % 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: 0.31 (0.22), residues: 1502 helix: 1.90 (0.26), residues: 404 sheet: -0.57 (0.27), residues: 351 loop : -0.27 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS R 95 PHE 0.015 0.001 PHE N 108 TYR 0.015 0.001 TYR R 82 ARG 0.003 0.000 ARG Y 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 7) link_NAG-ASN : angle 1.42142 ( 21) hydrogen bonds : bond 0.04329 ( 491) hydrogen bonds : angle 4.54922 ( 1356) SS BOND : bond 0.00398 ( 17) SS BOND : angle 1.58593 ( 34) covalent geometry : bond 0.00418 (12916) covalent geometry : angle 0.62627 (17568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.480 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7506 (tp40) cc_final: 0.7276 (mm110) REVERT: A 35 GLN cc_start: 0.8137 (tt0) cc_final: 0.7597 (mm-40) REVERT: A 58 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7183 (tptt) REVERT: A 236 GLN cc_start: 0.8368 (mt0) cc_final: 0.8164 (pt0) REVERT: A 301 TYR cc_start: 0.8362 (m-80) cc_final: 0.8125 (m-80) REVERT: A 346 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6693 (mtm-85) REVERT: B 23 LYS cc_start: 0.9253 (tptp) cc_final: 0.8918 (mtmt) REVERT: B 59 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: B 226 GLU cc_start: 0.7303 (pt0) cc_final: 0.7044 (pt0) REVERT: B 263 THR cc_start: 0.8666 (t) cc_final: 0.8355 (m) REVERT: B 303 ASP cc_start: 0.7317 (t0) cc_final: 0.6949 (m-30) REVERT: N 34 MET cc_start: 0.7868 (mmm) cc_final: 0.7646 (mmm) REVERT: N 83 MET cc_start: 0.6315 (ttm) cc_final: 0.5574 (ttm) REVERT: R 153 PHE cc_start: 0.7565 (m-80) cc_final: 0.6780 (p90) REVERT: R 403 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7184 (t0) REVERT: R 432 ASN cc_start: 0.8277 (m-40) cc_final: 0.7909 (m110) REVERT: R 453 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6721 (tpt) REVERT: R 651 LYS cc_start: 0.7308 (mttt) cc_final: 0.6771 (tppt) REVERT: R 677 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8548 (mp) REVERT: X 29 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7017 (mmm) REVERT: X 45 LYS cc_start: 0.8388 (pttm) cc_final: 0.8108 (pmtt) REVERT: X 47 MET cc_start: 0.8831 (mtt) cc_final: 0.8547 (mtt) REVERT: X 71 MET cc_start: 0.4343 (pmm) cc_final: 0.4058 (pmm) REVERT: X 91 LYS cc_start: 0.7839 (mttp) cc_final: 0.7491 (mtmt) REVERT: Y 52 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7280 (tmm) REVERT: Y 70 ASP cc_start: 0.8271 (m-30) cc_final: 0.7636 (t0) outliers start: 42 outliers final: 27 residues processed: 168 average time/residue: 1.0013 time to fit residues: 189.0784 Evaluate side-chains 169 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 257 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain R residue 453 MET Chi-restraints excluded: chain R residue 494 CYS Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 580 LEU Chi-restraints excluded: chain R residue 677 LEU Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 29 MET Chi-restraints excluded: chain Y residue 30 HIS Chi-restraints excluded: chain Y residue 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 0.0170 chunk 22 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 111 optimal weight: 0.0010 chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.4224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 239 ASN R 248 HIS R 271 HIS ** X 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.204431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147802 restraints weight = 14570.613| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.54 r_work: 0.3534 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12940 Z= 0.110 Angle : 0.582 12.478 17623 Z= 0.297 Chirality : 0.042 0.198 2039 Planarity : 0.004 0.051 2132 Dihedral : 6.504 58.940 2814 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.27 % Allowed : 19.64 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1502 helix: 2.21 (0.26), residues: 404 sheet: -0.60 (0.27), residues: 343 loop : -0.15 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS Y 30 PHE 0.010 0.001 PHE B 199 TYR 0.014 0.001 TYR R 82 ARG 0.007 0.000 ARG Y 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 7) link_NAG-ASN : angle 1.21748 ( 21) hydrogen bonds : bond 0.03736 ( 491) hydrogen bonds : angle 4.41912 ( 1356) SS BOND : bond 0.00244 ( 17) SS BOND : angle 1.44569 ( 34) covalent geometry : bond 0.00250 (12916) covalent geometry : angle 0.57830 (17568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8401.62 seconds wall clock time: 144 minutes 9.71 seconds (8649.71 seconds total)