Starting phenix.real_space_refine on Tue Jul 29 17:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iyc_9751/07_2025/6iyc_9751.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iyc_9751/07_2025/6iyc_9751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6iyc_9751/07_2025/6iyc_9751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iyc_9751/07_2025/6iyc_9751.map" model { file = "/net/cci-nas-00/data/ceres_data/6iyc_9751/07_2025/6iyc_9751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iyc_9751/07_2025/6iyc_9751.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 43 5.16 5 C 7236 2.51 5 N 1748 2.21 5 O 2008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 11037 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2407 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 226 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "F" 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: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" 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: "I" 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: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.98, per 1000 atoms: 0.63 Number of scatterers: 11037 At special positions: 0 Unit cell: (109.1, 94.917, 134.193, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 2 15.00 O 2008 8.00 N 1748 7.00 C 7236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.01 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.02 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=2, symmetry=0 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 817 " - " ASN A 464 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG A 821 " - " ASN A 580 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 59.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.305A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.779A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.757A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.745A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.538A pdb=" N TYR A 173 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.859A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.338A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.682A pdb=" N SER A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.857A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.513A pdb=" N ARG A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 387 through 405 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.865A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.709A pdb=" N LEU A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.524A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.630A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.646A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.536A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 74 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.833A pdb=" N THR B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 108 " --> pdb=" O PHE B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.571A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.735A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.524A pdb=" N TYR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.654A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 removed outlier: 4.209A pdb=" N ARG B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.606A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 429 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.006A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.639A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 30 through 61 removed outlier: 3.792A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.875A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 135 removed outlier: 3.510A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.914A pdb=" N LEU C 142 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 143 " --> pdb=" O ASP C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 139 through 143' Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.738A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.627A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 removed outlier: 3.804A pdb=" N ASN C 207 " --> pdb=" O THR C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.504A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 21 removed outlier: 4.218A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 26 through 43 removed outlier: 3.723A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 82 removed outlier: 4.083A pdb=" N ILE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'E' and resid 14 through 26 removed outlier: 3.753A pdb=" N LEU E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.770A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 74 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.944A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.144A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.526A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.147A pdb=" N VAL E 34 " --> pdb=" O GLY B 382 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1674 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: 3.48 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1777 1.32 - 1.44: 3104 1.44 - 1.56: 6356 1.56 - 1.69: 7 1.69 - 1.81: 66 Bond restraints: 11310 Sorted by residual: bond pdb=" CB CYS A 248 " pdb=" SG CYS A 248 " ideal model delta sigma weight residual 1.808 1.694 0.114 3.30e-02 9.18e+02 1.20e+01 bond pdb=" C1 BMA G 5 " pdb=" C2 BMA G 5 " ideal model delta sigma weight residual 1.519 1.577 -0.058 2.00e-02 2.50e+03 8.50e+00 bond pdb=" C1 BMA G 5 " pdb=" O5 BMA G 5 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" CG LEU A 121 " pdb=" CD2 LEU A 121 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.90e+00 bond pdb=" CB VAL A 147 " pdb=" CG1 VAL A 147 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.45e+00 ... (remaining 11305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 14584 2.38 - 4.77: 704 4.77 - 7.15: 98 7.15 - 9.54: 33 9.54 - 11.92: 7 Bond angle restraints: 15426 Sorted by residual: angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" CB PRO B 117 " ideal model delta sigma weight residual 103.25 111.51 -8.26 1.05e+00 9.07e-01 6.19e+01 angle pdb=" C PRO A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 119.84 112.10 7.74 1.25e+00 6.40e-01 3.84e+01 angle pdb=" N ARG A 434 " pdb=" CA ARG A 434 " pdb=" C ARG A 434 " ideal model delta sigma weight residual 114.62 120.57 -5.95 1.14e+00 7.69e-01 2.72e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 109.81 120.48 -10.67 2.21e+00 2.05e-01 2.33e+01 angle pdb=" N TRP A 289 " pdb=" CA TRP A 289 " pdb=" C TRP A 289 " ideal model delta sigma weight residual 110.97 116.12 -5.15 1.09e+00 8.42e-01 2.23e+01 ... (remaining 15421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 6674 22.52 - 45.04: 269 45.04 - 67.57: 50 67.57 - 90.09: 32 90.09 - 112.61: 18 Dihedral angle restraints: 7043 sinusoidal: 3095 harmonic: 3948 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -172.35 86.35 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -171.09 85.09 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -138.82 -41.18 0 5.00e+00 4.00e-02 6.78e+01 ... (remaining 7040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1607 0.095 - 0.190: 221 0.190 - 0.284: 28 0.284 - 0.379: 3 0.379 - 0.474: 3 Chirality restraints: 1862 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.02 -0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C1 NAG A 810 " pdb=" ND2 ASN A 387 " pdb=" C2 NAG A 810 " pdb=" O5 NAG A 810 " both_signs ideal model delta sigma weight residual False -2.40 -2.84 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 562 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1859 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 580 " 0.040 2.00e-02 2.50e+03 2.65e-01 8.80e+02 pdb=" CG ASN A 580 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 580 " -0.238 2.00e-02 2.50e+03 pdb=" ND2 ASN A 580 " 0.439 2.00e-02 2.50e+03 pdb=" C1 NAG A 821 " -0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 387 " -0.055 2.00e-02 2.50e+03 6.25e-02 4.88e+01 pdb=" CG ASN A 387 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 387 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 387 " 0.093 2.00e-02 2.50e+03 pdb=" C1 NAG A 810 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 810 " 0.050 2.00e-02 2.50e+03 4.06e-02 2.06e+01 pdb=" C7 NAG A 810 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG A 810 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG A 810 " -0.064 2.00e-02 2.50e+03 pdb=" O7 NAG A 810 " -0.010 2.00e-02 2.50e+03 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 87 2.62 - 3.19: 9180 3.19 - 3.76: 16760 3.76 - 4.33: 23330 4.33 - 4.90: 38431 Nonbonded interactions: 87788 Sorted by model distance: nonbonded pdb=" O3 NAG A 810 " pdb=" O7 NAG A 810 " model vdw 2.053 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A 100 " pdb=" OH TYR A 457 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.281 3.040 ... (remaining 87783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.240 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.011 0.114 11337 Z= 0.469 Angle : 1.240 17.647 15497 Z= 0.623 Chirality : 0.070 0.474 1862 Planarity : 0.008 0.079 1860 Dihedral : 15.023 112.609 4485 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.46 % Favored : 92.32 % Rotamer: Outliers : 0.88 % Allowed : 3.68 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.39 % Twisted General : 0.54 % 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: -3.74 (0.18), residues: 1341 helix: -2.11 (0.15), residues: 723 sheet: -1.59 (0.45), residues: 115 loop : -3.09 (0.21), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.005 TRP C 227 HIS 0.020 0.005 HIS C 197 PHE 0.050 0.005 PHE A 448 TYR 0.036 0.004 TYR C 90 ARG 0.016 0.002 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.02946 ( 12) link_NAG-ASN : angle 6.40460 ( 36) link_BETA1-4 : bond 0.00758 ( 7) link_BETA1-4 : angle 3.21341 ( 21) hydrogen bonds : bond 0.18117 ( 587) hydrogen bonds : angle 6.58638 ( 1674) link_BETA1-6 : bond 0.00614 ( 1) link_BETA1-6 : angle 1.29000 ( 3) SS BOND : bond 0.01117 ( 4) SS BOND : angle 2.86139 ( 8) link_BETA1-3 : bond 0.01258 ( 1) link_BETA1-3 : angle 0.97003 ( 3) covalent geometry : bond 0.01124 (11310) covalent geometry : angle 1.19627 (15426) Misc. bond : bond 0.00237 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9133 (mmp) cc_final: 0.8554 (mmm) REVERT: A 617 LEU cc_start: 0.8875 (mt) cc_final: 0.8642 (mt) REVERT: A 650 GLU cc_start: 0.8429 (tt0) cc_final: 0.8002 (tt0) REVERT: B 84 MET cc_start: 0.8629 (mtt) cc_final: 0.8329 (mtp) REVERT: B 248 LEU cc_start: 0.8831 (mt) cc_final: 0.8555 (mp) REVERT: B 252 VAL cc_start: 0.8996 (t) cc_final: 0.8613 (m) REVERT: B 255 VAL cc_start: 0.9113 (t) cc_final: 0.8900 (m) REVERT: C 180 ASP cc_start: 0.8414 (t70) cc_final: 0.8172 (t0) REVERT: D 39 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7492 (tpp80) REVERT: E 1 LEU cc_start: 0.8511 (tp) cc_final: 0.8279 (tp) outliers start: 10 outliers final: 7 residues processed: 256 average time/residue: 1.1807 time to fit residues: 326.1112 Evaluate side-chains 146 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 142 ASN A 158 HIS A 163 GLN A 305 GLN A 358 ASN A 385 GLN A 454 GLN A 531 ASN A 606 GLN B 214 HIS B 222 GLN C 116 GLN D 79 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088363 restraints weight = 16512.796| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.29 r_work: 0.3006 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11337 Z= 0.156 Angle : 0.761 11.046 15497 Z= 0.367 Chirality : 0.049 0.461 1862 Planarity : 0.005 0.057 1860 Dihedral : 13.613 115.133 2162 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 3.95 % Allowed : 11.14 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.22), residues: 1341 helix: 0.02 (0.19), residues: 727 sheet: -1.53 (0.43), residues: 128 loop : -2.47 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 227 HIS 0.005 0.001 HIS A 449 PHE 0.034 0.002 PHE A 302 TYR 0.017 0.002 TYR A 569 ARG 0.007 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 12) link_NAG-ASN : angle 3.27077 ( 36) link_BETA1-4 : bond 0.00559 ( 7) link_BETA1-4 : angle 1.78100 ( 21) hydrogen bonds : bond 0.05055 ( 587) hydrogen bonds : angle 4.46779 ( 1674) link_BETA1-6 : bond 0.01642 ( 1) link_BETA1-6 : angle 2.12236 ( 3) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.74106 ( 8) link_BETA1-3 : bond 0.01499 ( 1) link_BETA1-3 : angle 1.05498 ( 3) covalent geometry : bond 0.00354 (11310) covalent geometry : angle 0.74137 (15426) Misc. bond : bond 0.00863 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.9218 (mmp) cc_final: 0.8876 (mmm) REVERT: A 237 GLN cc_start: 0.7313 (tm-30) cc_final: 0.7005 (tm-30) REVERT: A 317 ASP cc_start: 0.7432 (t70) cc_final: 0.6993 (t0) REVERT: A 364 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: A 540 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: A 598 ASP cc_start: 0.8052 (t70) cc_final: 0.7847 (t70) REVERT: A 617 LEU cc_start: 0.8757 (mt) cc_final: 0.8470 (mt) REVERT: B 84 MET cc_start: 0.8875 (mtt) cc_final: 0.8560 (mtp) REVERT: B 146 MET cc_start: 0.7294 (tpt) cc_final: 0.7092 (tpt) REVERT: B 153 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7598 (tp) REVERT: B 165 TRP cc_start: 0.8834 (t60) cc_final: 0.8553 (t60) REVERT: B 252 VAL cc_start: 0.9017 (t) cc_final: 0.8715 (m) REVERT: C 240 GLN cc_start: 0.8446 (mt0) cc_final: 0.8218 (mm-40) REVERT: D 8 ASN cc_start: 0.8121 (p0) cc_final: 0.7814 (p0) REVERT: D 39 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7610 (tpp80) REVERT: D 40 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7701 (tm-30) REVERT: D 91 TYR cc_start: 0.8802 (m-80) cc_final: 0.8487 (m-80) outliers start: 45 outliers final: 10 residues processed: 187 average time/residue: 1.2435 time to fit residues: 252.6796 Evaluate side-chains 151 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 263 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 72 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 516 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085097 restraints weight = 16760.281| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.25 r_work: 0.2948 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11337 Z= 0.213 Angle : 0.761 10.978 15497 Z= 0.367 Chirality : 0.050 0.533 1862 Planarity : 0.005 0.062 1860 Dihedral : 12.086 114.837 2159 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.82 % Favored : 94.11 % Rotamer: Outliers : 4.30 % Allowed : 13.68 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.16 % 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: -0.76 (0.23), residues: 1341 helix: 0.75 (0.20), residues: 721 sheet: -1.10 (0.46), residues: 115 loop : -2.24 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 58 HIS 0.007 0.001 HIS A 449 PHE 0.035 0.002 PHE A 302 TYR 0.018 0.002 TYR A 569 ARG 0.007 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 12) link_NAG-ASN : angle 3.09550 ( 36) link_BETA1-4 : bond 0.00432 ( 7) link_BETA1-4 : angle 2.05330 ( 21) hydrogen bonds : bond 0.05101 ( 587) hydrogen bonds : angle 4.21034 ( 1674) link_BETA1-6 : bond 0.01861 ( 1) link_BETA1-6 : angle 2.02719 ( 3) SS BOND : bond 0.00449 ( 4) SS BOND : angle 1.41335 ( 8) link_BETA1-3 : bond 0.01437 ( 1) link_BETA1-3 : angle 0.79415 ( 3) covalent geometry : bond 0.00506 (11310) covalent geometry : angle 0.74275 (15426) Misc. bond : bond 0.00556 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9229 (mmp) cc_final: 0.8810 (mmm) REVERT: A 237 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 317 ASP cc_start: 0.7622 (t70) cc_final: 0.7148 (t0) REVERT: A 598 ASP cc_start: 0.8092 (t70) cc_final: 0.7865 (t70) REVERT: A 617 LEU cc_start: 0.8792 (mt) cc_final: 0.8509 (mt) REVERT: B 84 MET cc_start: 0.8938 (mtt) cc_final: 0.8600 (mtp) REVERT: B 146 MET cc_start: 0.7208 (tpt) cc_final: 0.6892 (tpp) REVERT: B 252 VAL cc_start: 0.9031 (t) cc_final: 0.8772 (m) REVERT: B 273 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6693 (mt-10) REVERT: C 109 ARG cc_start: 0.6788 (pmm150) cc_final: 0.6554 (pmm150) REVERT: C 240 GLN cc_start: 0.8543 (mt0) cc_final: 0.8173 (mm-40) REVERT: D 8 ASN cc_start: 0.8086 (p0) cc_final: 0.7702 (p0) REVERT: D 39 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7539 (tpp80) REVERT: D 58 TRP cc_start: 0.7390 (OUTLIER) cc_final: 0.7189 (t60) REVERT: D 91 TYR cc_start: 0.8844 (m-80) cc_final: 0.8442 (m-80) outliers start: 49 outliers final: 25 residues processed: 177 average time/residue: 1.1593 time to fit residues: 223.0270 Evaluate side-chains 163 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.086804 restraints weight = 16561.380| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.26 r_work: 0.2975 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11337 Z= 0.145 Angle : 0.679 11.662 15497 Z= 0.327 Chirality : 0.046 0.446 1862 Planarity : 0.004 0.057 1860 Dihedral : 11.168 112.933 2159 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 3.42 % Allowed : 15.26 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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: -0.27 (0.23), residues: 1341 helix: 1.24 (0.20), residues: 716 sheet: -1.07 (0.43), residues: 134 loop : -2.11 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 58 HIS 0.004 0.001 HIS A 449 PHE 0.033 0.002 PHE A 302 TYR 0.017 0.001 TYR D 47 ARG 0.007 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 12) link_NAG-ASN : angle 2.57281 ( 36) link_BETA1-4 : bond 0.00476 ( 7) link_BETA1-4 : angle 1.87570 ( 21) hydrogen bonds : bond 0.04330 ( 587) hydrogen bonds : angle 4.06223 ( 1674) link_BETA1-6 : bond 0.01785 ( 1) link_BETA1-6 : angle 2.40362 ( 3) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.99672 ( 8) link_BETA1-3 : bond 0.01166 ( 1) link_BETA1-3 : angle 1.17520 ( 3) covalent geometry : bond 0.00332 (11310) covalent geometry : angle 0.66367 (15426) Misc. bond : bond 0.00341 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8638 (mppt) REVERT: A 231 MET cc_start: 0.9230 (mmp) cc_final: 0.8784 (mmm) REVERT: A 237 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 317 ASP cc_start: 0.7471 (t70) cc_final: 0.7055 (t0) REVERT: A 548 ASP cc_start: 0.8194 (m-30) cc_final: 0.7992 (m-30) REVERT: A 598 ASP cc_start: 0.8090 (t70) cc_final: 0.7849 (t70) REVERT: B 84 MET cc_start: 0.8930 (mtt) cc_final: 0.8662 (mtp) REVERT: B 146 MET cc_start: 0.7363 (tpt) cc_final: 0.7105 (tpt) REVERT: B 233 MET cc_start: 0.9276 (mmm) cc_final: 0.9054 (tpt) REVERT: B 252 VAL cc_start: 0.9045 (t) cc_final: 0.8775 (m) REVERT: B 273 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6630 (mt-10) REVERT: C 187 TYR cc_start: 0.8399 (m-80) cc_final: 0.8073 (m-10) REVERT: C 240 GLN cc_start: 0.8553 (mt0) cc_final: 0.8212 (mm-40) REVERT: D 8 ASN cc_start: 0.8077 (p0) cc_final: 0.7692 (p0) REVERT: D 39 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7621 (tpp80) REVERT: D 58 TRP cc_start: 0.7169 (OUTLIER) cc_final: 0.6957 (t60) REVERT: E 25 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7311 (pt) outliers start: 39 outliers final: 22 residues processed: 173 average time/residue: 1.1329 time to fit residues: 213.1666 Evaluate side-chains 162 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 38 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087206 restraints weight = 16573.470| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.26 r_work: 0.2979 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11337 Z= 0.135 Angle : 0.656 12.457 15497 Z= 0.317 Chirality : 0.045 0.421 1862 Planarity : 0.004 0.053 1860 Dihedral : 10.696 111.362 2158 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 3.86 % Allowed : 15.79 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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: 0.08 (0.23), residues: 1341 helix: 1.49 (0.20), residues: 722 sheet: -0.92 (0.47), residues: 124 loop : -1.90 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 58 HIS 0.004 0.001 HIS A 449 PHE 0.031 0.001 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.008 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 12) link_NAG-ASN : angle 2.43078 ( 36) link_BETA1-4 : bond 0.00458 ( 7) link_BETA1-4 : angle 1.79467 ( 21) hydrogen bonds : bond 0.04123 ( 587) hydrogen bonds : angle 3.99636 ( 1674) link_BETA1-6 : bond 0.01683 ( 1) link_BETA1-6 : angle 2.39549 ( 3) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.93519 ( 8) link_BETA1-3 : bond 0.01100 ( 1) link_BETA1-3 : angle 1.30208 ( 3) covalent geometry : bond 0.00306 (11310) covalent geometry : angle 0.64177 (15426) Misc. bond : bond 0.00624 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8656 (mppt) REVERT: A 138 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.8939 (m) REVERT: A 231 MET cc_start: 0.9228 (mmp) cc_final: 0.8751 (mmm) REVERT: A 237 GLN cc_start: 0.7255 (tm-30) cc_final: 0.7048 (tm-30) REVERT: A 317 ASP cc_start: 0.7453 (t70) cc_final: 0.7019 (t0) REVERT: A 548 ASP cc_start: 0.8212 (m-30) cc_final: 0.7986 (m-30) REVERT: A 598 ASP cc_start: 0.8114 (t70) cc_final: 0.7867 (t70) REVERT: B 84 MET cc_start: 0.8912 (mtt) cc_final: 0.8577 (mtp) REVERT: B 146 MET cc_start: 0.7441 (tpt) cc_final: 0.7174 (tpp) REVERT: B 149 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 248 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 252 VAL cc_start: 0.9042 (t) cc_final: 0.8779 (m) REVERT: B 454 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: C 109 ARG cc_start: 0.6819 (pmm150) cc_final: 0.6584 (pmm150) REVERT: C 183 GLU cc_start: 0.8300 (tp30) cc_final: 0.8075 (mm-30) REVERT: C 187 TYR cc_start: 0.8437 (m-80) cc_final: 0.8095 (m-10) REVERT: C 240 GLN cc_start: 0.8563 (mt0) cc_final: 0.8222 (mm-40) REVERT: D 8 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7702 (p0) REVERT: D 39 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7526 (tpp80) REVERT: D 58 TRP cc_start: 0.7094 (OUTLIER) cc_final: 0.6801 (t60) REVERT: E 25 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7286 (pt) outliers start: 44 outliers final: 23 residues processed: 175 average time/residue: 1.2456 time to fit residues: 238.1137 Evaluate side-chains 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.083350 restraints weight = 16768.211| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.27 r_work: 0.2915 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11337 Z= 0.257 Angle : 0.778 12.679 15497 Z= 0.375 Chirality : 0.051 0.494 1862 Planarity : 0.005 0.059 1860 Dihedral : 10.921 112.678 2158 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 4.56 % Allowed : 15.09 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1341 helix: 1.34 (0.20), residues: 723 sheet: -0.85 (0.46), residues: 127 loop : -1.94 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 58 HIS 0.009 0.001 HIS A 449 PHE 0.032 0.002 PHE A 302 TYR 0.020 0.002 TYR A 173 ARG 0.006 0.001 ARG A 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 12) link_NAG-ASN : angle 3.00704 ( 36) link_BETA1-4 : bond 0.00404 ( 7) link_BETA1-4 : angle 2.16981 ( 21) hydrogen bonds : bond 0.05118 ( 587) hydrogen bonds : angle 4.12590 ( 1674) link_BETA1-6 : bond 0.02013 ( 1) link_BETA1-6 : angle 2.06928 ( 3) SS BOND : bond 0.00632 ( 4) SS BOND : angle 1.65027 ( 8) link_BETA1-3 : bond 0.01149 ( 1) link_BETA1-3 : angle 1.33410 ( 3) covalent geometry : bond 0.00622 (11310) covalent geometry : angle 0.76072 (15426) Misc. bond : bond 0.00321 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8692 (mppt) REVERT: A 138 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.8969 (m) REVERT: A 231 MET cc_start: 0.9233 (mmp) cc_final: 0.8903 (tpt) REVERT: A 237 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 317 ASP cc_start: 0.7482 (t70) cc_final: 0.6988 (t0) REVERT: A 471 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8326 (pp) REVERT: A 548 ASP cc_start: 0.8294 (m-30) cc_final: 0.8077 (m-30) REVERT: A 598 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7951 (t70) REVERT: A 617 LEU cc_start: 0.8831 (mt) cc_final: 0.8547 (mt) REVERT: B 84 MET cc_start: 0.8960 (mtt) cc_final: 0.8695 (mtp) REVERT: B 146 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7121 (tpp) REVERT: B 252 VAL cc_start: 0.9062 (t) cc_final: 0.8799 (m) REVERT: C 187 TYR cc_start: 0.8465 (m-80) cc_final: 0.8127 (m-10) REVERT: C 240 GLN cc_start: 0.8604 (mt0) cc_final: 0.8262 (mm-40) REVERT: D 8 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7779 (p0) REVERT: D 39 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7540 (tpp80) REVERT: D 47 TYR cc_start: 0.6508 (t80) cc_final: 0.6291 (t80) REVERT: E 25 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7429 (pt) outliers start: 52 outliers final: 27 residues processed: 175 average time/residue: 2.0501 time to fit residues: 389.3038 Evaluate side-chains 166 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 35 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0170 chunk 100 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 204 ASN C 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087086 restraints weight = 16677.072| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.33 r_work: 0.2983 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11337 Z= 0.123 Angle : 0.664 12.889 15497 Z= 0.318 Chirality : 0.046 0.571 1862 Planarity : 0.004 0.056 1860 Dihedral : 10.347 109.232 2158 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.30 % Rotamer: Outliers : 2.63 % Allowed : 17.54 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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 (0.24), residues: 1341 helix: 1.69 (0.20), residues: 720 sheet: -0.74 (0.47), residues: 124 loop : -1.76 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 58 HIS 0.004 0.001 HIS A 553 PHE 0.032 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.010 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 12) link_NAG-ASN : angle 2.28965 ( 36) link_BETA1-4 : bond 0.00514 ( 7) link_BETA1-4 : angle 1.70870 ( 21) hydrogen bonds : bond 0.03929 ( 587) hydrogen bonds : angle 3.96401 ( 1674) link_BETA1-6 : bond 0.01587 ( 1) link_BETA1-6 : angle 2.36649 ( 3) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.92191 ( 8) link_BETA1-3 : bond 0.01081 ( 1) link_BETA1-3 : angle 1.40973 ( 3) covalent geometry : bond 0.00272 (11310) covalent geometry : angle 0.65202 (15426) Misc. bond : bond 0.00733 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8582 (mppt) REVERT: A 108 MET cc_start: 0.9244 (mmm) cc_final: 0.9025 (mmm) REVERT: A 231 MET cc_start: 0.9201 (mmp) cc_final: 0.8698 (mmm) REVERT: A 317 ASP cc_start: 0.7507 (t70) cc_final: 0.7097 (t0) REVERT: A 548 ASP cc_start: 0.8299 (m-30) cc_final: 0.8072 (m-30) REVERT: A 598 ASP cc_start: 0.8135 (t70) cc_final: 0.7846 (t70) REVERT: B 84 MET cc_start: 0.8936 (mtt) cc_final: 0.8656 (mtp) REVERT: B 146 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7102 (tpp) REVERT: B 248 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8215 (mp) REVERT: B 252 VAL cc_start: 0.8981 (t) cc_final: 0.8734 (m) REVERT: B 273 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6545 (pt0) REVERT: C 109 ARG cc_start: 0.6775 (pmm150) cc_final: 0.6528 (pmm150) REVERT: C 187 TYR cc_start: 0.8413 (m-80) cc_final: 0.8046 (m-10) REVERT: C 240 GLN cc_start: 0.8586 (mt0) cc_final: 0.8250 (mm-40) REVERT: D 8 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7666 (p0) REVERT: D 39 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7500 (tpp80) REVERT: E 25 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7307 (pt) outliers start: 30 outliers final: 17 residues processed: 162 average time/residue: 1.2755 time to fit residues: 224.7929 Evaluate side-chains 152 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083960 restraints weight = 16513.517| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.30 r_work: 0.2927 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11337 Z= 0.223 Angle : 0.759 13.911 15497 Z= 0.364 Chirality : 0.050 0.597 1862 Planarity : 0.005 0.056 1860 Dihedral : 10.530 109.067 2158 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 2.81 % Allowed : 17.63 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1341 helix: 1.55 (0.20), residues: 723 sheet: -0.64 (0.47), residues: 125 loop : -1.85 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 58 HIS 0.007 0.001 HIS A 449 PHE 0.031 0.002 PHE A 302 TYR 0.020 0.002 TYR A 173 ARG 0.005 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 12) link_NAG-ASN : angle 2.82445 ( 36) link_BETA1-4 : bond 0.00379 ( 7) link_BETA1-4 : angle 2.03799 ( 21) hydrogen bonds : bond 0.04834 ( 587) hydrogen bonds : angle 4.06220 ( 1674) link_BETA1-6 : bond 0.01769 ( 1) link_BETA1-6 : angle 2.15788 ( 3) SS BOND : bond 0.00512 ( 4) SS BOND : angle 1.45815 ( 8) link_BETA1-3 : bond 0.01044 ( 1) link_BETA1-3 : angle 1.68072 ( 3) covalent geometry : bond 0.00534 (11310) covalent geometry : angle 0.74309 (15426) Misc. bond : bond 0.00405 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8613 (mppt) REVERT: A 108 MET cc_start: 0.9254 (mmm) cc_final: 0.9029 (mmm) REVERT: A 138 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.8967 (m) REVERT: A 231 MET cc_start: 0.9201 (mmp) cc_final: 0.8868 (tpt) REVERT: A 317 ASP cc_start: 0.7515 (t70) cc_final: 0.7050 (t0) REVERT: A 548 ASP cc_start: 0.8328 (m-30) cc_final: 0.8104 (m-30) REVERT: A 591 LYS cc_start: 0.8805 (mmpt) cc_final: 0.8332 (mmmm) REVERT: A 598 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7930 (t70) REVERT: B 84 MET cc_start: 0.8957 (mtt) cc_final: 0.8685 (mtp) REVERT: B 146 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7105 (tpp) REVERT: B 248 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8272 (mp) REVERT: B 252 VAL cc_start: 0.8993 (t) cc_final: 0.8741 (m) REVERT: C 109 ARG cc_start: 0.6810 (pmm150) cc_final: 0.6541 (pmm150) REVERT: C 183 GLU cc_start: 0.8273 (tp30) cc_final: 0.7938 (mm-30) REVERT: C 187 TYR cc_start: 0.8461 (m-80) cc_final: 0.8135 (m-10) REVERT: C 240 GLN cc_start: 0.8586 (mt0) cc_final: 0.8275 (mm-40) REVERT: D 8 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7908 (p0) REVERT: D 39 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7547 (tpp80) REVERT: E 25 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7461 (pt) outliers start: 32 outliers final: 21 residues processed: 159 average time/residue: 1.0880 time to fit residues: 188.6470 Evaluate side-chains 159 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085301 restraints weight = 16628.112| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.31 r_work: 0.2946 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11337 Z= 0.168 Angle : 0.713 12.806 15497 Z= 0.342 Chirality : 0.047 0.505 1862 Planarity : 0.004 0.056 1860 Dihedral : 10.280 107.025 2158 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 2.81 % Allowed : 18.42 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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 (0.23), residues: 1341 helix: 1.68 (0.20), residues: 720 sheet: -0.60 (0.48), residues: 125 loop : -1.83 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 58 HIS 0.005 0.001 HIS A 449 PHE 0.032 0.002 PHE A 302 TYR 0.016 0.002 TYR A 569 ARG 0.010 0.001 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 12) link_NAG-ASN : angle 2.52477 ( 36) link_BETA1-4 : bond 0.00407 ( 7) link_BETA1-4 : angle 1.84924 ( 21) hydrogen bonds : bond 0.04383 ( 587) hydrogen bonds : angle 4.01509 ( 1674) link_BETA1-6 : bond 0.01673 ( 1) link_BETA1-6 : angle 2.33916 ( 3) SS BOND : bond 0.00383 ( 4) SS BOND : angle 1.12207 ( 8) link_BETA1-3 : bond 0.01042 ( 1) link_BETA1-3 : angle 1.68949 ( 3) covalent geometry : bond 0.00397 (11310) covalent geometry : angle 0.69939 (15426) Misc. bond : bond 0.00326 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8604 (mppt) REVERT: A 108 MET cc_start: 0.9221 (mmm) cc_final: 0.9013 (mmm) REVERT: A 138 VAL cc_start: 0.9318 (OUTLIER) cc_final: 0.8943 (m) REVERT: A 231 MET cc_start: 0.9219 (mmp) cc_final: 0.8752 (mmm) REVERT: A 317 ASP cc_start: 0.7512 (t70) cc_final: 0.7086 (t0) REVERT: A 548 ASP cc_start: 0.8314 (m-30) cc_final: 0.8068 (m-30) REVERT: A 591 LYS cc_start: 0.8878 (mmpt) cc_final: 0.8398 (mmmm) REVERT: B 84 MET cc_start: 0.8951 (mtt) cc_final: 0.8669 (mtp) REVERT: B 146 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7062 (tpp) REVERT: B 248 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 252 VAL cc_start: 0.8967 (t) cc_final: 0.8665 (m) REVERT: B 273 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6624 (pt0) REVERT: C 99 GLU cc_start: 0.7910 (tt0) cc_final: 0.7096 (pt0) REVERT: C 183 GLU cc_start: 0.8279 (tp30) cc_final: 0.8025 (mm-30) REVERT: C 187 TYR cc_start: 0.8405 (m-80) cc_final: 0.8051 (m-10) REVERT: C 240 GLN cc_start: 0.8572 (mt0) cc_final: 0.8261 (mm-40) REVERT: D 8 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7680 (p0) REVERT: D 39 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7521 (tpp80) REVERT: E 25 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7439 (pt) outliers start: 32 outliers final: 24 residues processed: 160 average time/residue: 1.0972 time to fit residues: 191.5161 Evaluate side-chains 161 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087328 restraints weight = 16568.201| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.30 r_work: 0.2985 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 0.003 0.037 11337 Z= 0.128 Angle : 0.676 11.508 15497 Z= 0.323 Chirality : 0.045 0.443 1862 Planarity : 0.004 0.053 1860 Dihedral : 9.885 103.323 2158 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.37 % Allowed : 18.51 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1341 helix: 1.87 (0.20), residues: 719 sheet: -0.51 (0.49), residues: 125 loop : -1.76 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 58 HIS 0.004 0.001 HIS A 553 PHE 0.032 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.007 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 12) link_NAG-ASN : angle 2.23727 ( 36) link_BETA1-4 : bond 0.00464 ( 7) link_BETA1-4 : angle 1.65852 ( 21) hydrogen bonds : bond 0.03853 ( 587) hydrogen bonds : angle 3.93708 ( 1674) link_BETA1-6 : bond 0.01423 ( 1) link_BETA1-6 : angle 2.48285 ( 3) SS BOND : bond 0.00261 ( 4) SS BOND : angle 0.92815 ( 8) link_BETA1-3 : bond 0.01017 ( 1) link_BETA1-3 : angle 1.55478 ( 3) covalent geometry : bond 0.00292 (11310) covalent geometry : angle 0.66462 (15426) Misc. bond : bond 0.00280 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8514 (mppt) REVERT: A 138 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.8925 (m) REVERT: A 231 MET cc_start: 0.9203 (mmp) cc_final: 0.8729 (mmm) REVERT: A 317 ASP cc_start: 0.7468 (t70) cc_final: 0.7067 (t0) REVERT: A 548 ASP cc_start: 0.8309 (m-30) cc_final: 0.8041 (m-30) REVERT: A 591 LYS cc_start: 0.8891 (mmpt) cc_final: 0.8424 (mmmm) REVERT: B 84 MET cc_start: 0.8891 (mtt) cc_final: 0.8530 (mtp) REVERT: B 146 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.7058 (tpp) REVERT: B 252 VAL cc_start: 0.8977 (t) cc_final: 0.8677 (m) REVERT: B 273 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6606 (pt0) REVERT: C 99 GLU cc_start: 0.7875 (tt0) cc_final: 0.7067 (pt0) REVERT: C 183 GLU cc_start: 0.8266 (tp30) cc_final: 0.7951 (mm-30) REVERT: C 187 TYR cc_start: 0.8347 (m-80) cc_final: 0.7979 (m-10) REVERT: C 240 GLN cc_start: 0.8563 (mt0) cc_final: 0.8251 (mm-40) REVERT: D 8 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7610 (p0) REVERT: D 39 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7416 (mtp180) REVERT: E 25 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7351 (pt) outliers start: 27 outliers final: 19 residues processed: 151 average time/residue: 1.2236 time to fit residues: 201.0111 Evaluate side-chains 153 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 103 optimal weight: 0.1980 chunk 132 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.088846 restraints weight = 16446.352| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.29 r_work: 0.3011 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11337 Z= 0.118 Angle : 0.659 10.895 15497 Z= 0.317 Chirality : 0.044 0.421 1862 Planarity : 0.004 0.051 1860 Dihedral : 9.527 97.298 2158 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.00 % Rotamer: Outliers : 2.46 % Allowed : 18.42 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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: 0.69 (0.24), residues: 1341 helix: 2.01 (0.20), residues: 718 sheet: -0.58 (0.52), residues: 112 loop : -1.65 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 PHE 0.030 0.001 PHE A 302 TYR 0.027 0.001 TYR B 77 ARG 0.011 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 12) link_NAG-ASN : angle 2.09789 ( 36) link_BETA1-4 : bond 0.00450 ( 7) link_BETA1-4 : angle 1.56103 ( 21) hydrogen bonds : bond 0.03600 ( 587) hydrogen bonds : angle 3.88156 ( 1674) link_BETA1-6 : bond 0.01404 ( 1) link_BETA1-6 : angle 2.81169 ( 3) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.83770 ( 8) link_BETA1-3 : bond 0.00992 ( 1) link_BETA1-3 : angle 1.52058 ( 3) covalent geometry : bond 0.00264 (11310) covalent geometry : angle 0.64824 (15426) Misc. bond : bond 0.00263 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10332.99 seconds wall clock time: 182 minutes 45.62 seconds (10965.62 seconds total)