Starting phenix.real_space_refine on Sat Aug 23 08:38:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x53_38060/08_2025/8x53_38060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x53_38060/08_2025/8x53_38060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x53_38060/08_2025/8x53_38060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x53_38060/08_2025/8x53_38060.map" model { file = "/net/cci-nas-00/data/ceres_data/8x53_38060/08_2025/8x53_38060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x53_38060/08_2025/8x53_38060.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.015 sd= 0.177 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 3 5.49 5 S 41 5.16 5 C 7172 2.51 5 N 1729 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10947 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: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2424 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 142 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.47, per 1000 atoms: 0.23 Number of scatterers: 10947 At special positions: 0 Unit cell: (109.332, 94.1775, 130.982, 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 41 16.00 P 3 15.00 O 2002 8.00 N 1729 7.00 C 7172 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " 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 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 531.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 58.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 79 through 87 removed outlier: 4.052A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.949A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.599A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.889A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.767A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.073A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.555A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.699A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.724A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (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 637 removed outlier: 3.751A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.775A 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 78 through 103 removed outlier: 3.752A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.595A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 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: 3.921A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.978A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.626A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.904A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.738A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 3.535A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.768A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.871A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.661A 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 22 removed outlier: 3.791A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.592A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 81 removed outlier: 4.129A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'E' and resid 26 through 40 removed outlier: 4.464A pdb=" N ILE E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.765A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 94 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.480A 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: 3.549A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.509A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.193A 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: 6.552A 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 Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 433 580 hydrogen bonds defined for protein. 1680 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: 1.56 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 20 1.18 - 1.33: 2909 1.33 - 1.49: 3685 1.49 - 1.65: 4541 1.65 - 1.81: 64 Bond restraints: 11219 Sorted by residual: bond pdb=" C ILE B 437 " pdb=" O ILE B 437 " ideal model delta sigma weight residual 1.241 1.017 0.224 1.25e-02 6.40e+03 3.21e+02 bond pdb=" C ASN A 243 " pdb=" N PRO A 244 " ideal model delta sigma weight residual 1.329 1.520 -0.191 1.25e-02 6.40e+03 2.34e+02 bond pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 1.471 1.656 -0.186 1.27e-02 6.20e+03 2.14e+02 bond pdb=" C PRO B 436 " pdb=" O PRO B 436 " ideal model delta sigma weight residual 1.235 1.053 0.182 1.30e-02 5.92e+03 1.96e+02 bond pdb=" C ILE B 387 " pdb=" O ILE B 387 " ideal model delta sigma weight residual 1.233 1.064 0.170 1.22e-02 6.72e+03 1.94e+02 ... (remaining 11214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 15185 5.73 - 11.45: 85 11.45 - 17.18: 15 17.18 - 22.91: 2 22.91 - 28.63: 1 Bond angle restraints: 15288 Sorted by residual: angle pdb=" N GLY C 233 " pdb=" CA GLY C 233 " pdb=" C GLY C 233 " ideal model delta sigma weight residual 115.43 144.06 -28.63 1.41e+00 5.03e-01 4.12e+02 angle pdb=" C LEU B 432 " pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 119.98 137.64 -17.66 1.16e+00 7.43e-01 2.32e+02 angle pdb=" C THR B 116 " pdb=" N PRO B 117 " pdb=" CA PRO B 117 " ideal model delta sigma weight residual 121.65 135.78 -14.13 1.01e+00 9.80e-01 1.96e+02 angle pdb=" CA ASN A 243 " pdb=" C ASN A 243 " pdb=" N PRO A 244 " ideal model delta sigma weight residual 119.40 132.83 -13.43 1.32e+00 5.74e-01 1.04e+02 angle pdb=" N VAL E 44 " pdb=" CA VAL E 44 " pdb=" CB VAL E 44 " ideal model delta sigma weight residual 112.07 100.53 11.54 1.14e+00 7.69e-01 1.02e+02 ... (remaining 15283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 6644 23.50 - 46.99: 215 46.99 - 70.49: 52 70.49 - 93.99: 21 93.99 - 117.48: 18 Dihedral angle restraints: 6950 sinusoidal: 3066 harmonic: 3884 Sorted by residual: dihedral pdb=" C THR E 43 " pdb=" N THR E 43 " pdb=" CA THR E 43 " pdb=" CB THR E 43 " ideal model delta harmonic sigma weight residual -122.00 -150.95 28.95 0 2.50e+00 1.60e-01 1.34e+02 dihedral pdb=" C PHE B 386 " pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" CB PHE B 386 " ideal model delta harmonic sigma weight residual -122.60 -98.17 -24.43 0 2.50e+00 1.60e-01 9.55e+01 dihedral pdb=" N THR E 43 " pdb=" C THR E 43 " pdb=" CA THR E 43 " pdb=" CB THR E 43 " ideal model delta harmonic sigma weight residual 123.40 147.04 -23.64 0 2.50e+00 1.60e-01 8.94e+01 ... (remaining 6947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 1795 0.232 - 0.464: 27 0.464 - 0.695: 3 0.695 - 0.927: 2 0.927 - 1.159: 1 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CA THR E 43 " pdb=" N THR E 43 " pdb=" C THR E 43 " pdb=" CB THR E 43 " both_signs ideal model delta sigma weight residual False 2.53 1.37 1.16 2.00e-01 2.50e+01 3.36e+01 chirality pdb=" CB THR B 116 " pdb=" CA THR B 116 " pdb=" OG1 THR B 116 " pdb=" CG2 THR B 116 " both_signs ideal model delta sigma weight residual False 2.55 1.83 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA PRO B 433 " pdb=" N PRO B 433 " pdb=" C PRO B 433 " pdb=" CB PRO B 433 " both_signs ideal model delta sigma weight residual False 2.72 3.42 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 1825 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.116 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 573 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.188 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 112 " -0.024 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C GLN B 112 " 0.081 2.00e-02 2.50e+03 pdb=" O GLN B 112 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU B 113 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 116 " 0.022 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C THR B 116 " -0.072 2.00e-02 2.50e+03 pdb=" O THR B 116 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO B 117 " 0.024 2.00e-02 2.50e+03 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 3 2.26 - 2.92: 4406 2.92 - 3.58: 15321 3.58 - 4.24: 25312 4.24 - 4.90: 42665 Nonbonded interactions: 87707 Sorted by model distance: nonbonded pdb=" OD1 ASN A 573 " pdb=" C1 NAG I 1 " model vdw 1.597 2.776 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 389 " pdb=" O ALA B 434 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.264 3.040 nonbonded pdb=" O THR B 399 " pdb=" OG1 THR B 399 " model vdw 2.296 3.040 ... (remaining 87702 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5067 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 : 0.017 1.466 11244 Z= 0.938 Angle : 1.419 61.446 15359 Z= 0.770 Chirality : 0.080 1.159 1828 Planarity : 0.008 0.071 1848 Dihedral : 14.529 117.484 4436 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Rotamer: Outliers : 0.53 % Allowed : 2.28 % Favored : 97.19 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.18), residues: 1322 helix: -1.93 (0.14), residues: 729 sheet: -1.54 (0.47), residues: 114 loop : -2.93 (0.23), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 626 TYR 0.035 0.003 TYR A 565 PHE 0.060 0.003 PHE B 386 TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.01036 (11219) covalent geometry : angle 1.21244 (15288) SS BOND : bond 0.00703 ( 4) SS BOND : angle 2.39547 ( 8) hydrogen bonds : bond 0.19638 ( 580) hydrogen bonds : angle 7.19721 ( 1680) link_BETA1-3 : bond 0.00076 ( 1) link_BETA1-3 : angle 1.62421 ( 3) link_BETA1-4 : bond 0.00211 ( 7) link_BETA1-4 : angle 2.21398 ( 21) link_BETA1-6 : bond 0.00528 ( 1) link_BETA1-6 : angle 1.46127 ( 3) link_NAG-ASN : bond 0.42324 ( 12) link_NAG-ASN : angle 15.17694 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 209 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6346 (mmmm) cc_final: 0.5853 (mptp) REVERT: A 77 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6567 (mp0) REVERT: A 78 LYS cc_start: 0.6869 (ptpt) cc_final: 0.6473 (ptpp) REVERT: A 81 ASP cc_start: 0.5709 (m-30) cc_final: 0.5508 (m-30) REVERT: A 139 GLN cc_start: 0.7059 (tt0) cc_final: 0.6841 (tt0) REVERT: A 206 SER cc_start: 0.5959 (m) cc_final: 0.5677 (p) REVERT: A 245 GLU cc_start: 0.5521 (mm-30) cc_final: 0.5276 (mt-10) REVERT: A 357 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6636 (tt0) REVERT: A 374 LEU cc_start: 0.6454 (mt) cc_final: 0.6197 (mt) REVERT: A 384 SER cc_start: 0.7029 (t) cc_final: 0.6682 (m) REVERT: A 439 VAL cc_start: 0.6561 (t) cc_final: 0.6267 (p) REVERT: A 500 GLU cc_start: 0.6495 (mt-10) cc_final: 0.5963 (tm-30) REVERT: A 512 GLN cc_start: 0.7580 (tt0) cc_final: 0.7140 (tt0) REVERT: A 531 ASN cc_start: 0.6829 (m-40) cc_final: 0.6588 (m110) REVERT: A 535 GLN cc_start: 0.7007 (mt0) cc_final: 0.6788 (mm-40) REVERT: A 540 GLN cc_start: 0.7671 (tt0) cc_final: 0.7303 (tp40) REVERT: A 544 SER cc_start: 0.6582 (m) cc_final: 0.6335 (p) REVERT: A 652 ARG cc_start: 0.6231 (mtp85) cc_final: 0.6020 (mtt180) REVERT: B 80 LYS cc_start: 0.6252 (tptt) cc_final: 0.5887 (tptm) REVERT: B 160 LYS cc_start: 0.7145 (mttm) cc_final: 0.6034 (mppt) REVERT: B 191 VAL cc_start: 0.5840 (t) cc_final: 0.5618 (m) REVERT: C 10 THR cc_start: 0.5662 (t) cc_final: 0.5349 (p) REVERT: C 28 ASP cc_start: 0.6583 (m-30) cc_final: 0.6230 (t0) REVERT: C 48 LEU cc_start: 0.5717 (mt) cc_final: 0.5480 (tt) REVERT: C 211 GLU cc_start: 0.6342 (pt0) cc_final: 0.5591 (pm20) REVERT: D 40 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6121 (mp0) REVERT: D 84 ARG cc_start: 0.6739 (mtt90) cc_final: 0.6228 (mtt90) outliers start: 6 outliers final: 0 residues processed: 213 average time/residue: 0.4600 time to fit residues: 106.4575 Evaluate side-chains 129 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 237 GLN A 331 GLN A 355 GLN A 385 GLN A 531 ASN B 112 GLN B 405 ASN B 464 GLN C 68 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.179828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.135543 restraints weight = 11866.722| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.09 r_work: 0.3273 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11244 Z= 0.143 Angle : 0.698 13.742 15359 Z= 0.336 Chirality : 0.044 0.312 1828 Planarity : 0.005 0.066 1848 Dihedral : 12.699 104.602 2104 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.55 % Allowed : 7.99 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.22), residues: 1322 helix: 0.28 (0.19), residues: 731 sheet: -1.19 (0.48), residues: 108 loop : -2.32 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 626 TYR 0.014 0.002 TYR A 565 PHE 0.037 0.002 PHE A 302 TRP 0.015 0.001 TRP C 227 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00308 (11219) covalent geometry : angle 0.66868 (15288) SS BOND : bond 0.00590 ( 4) SS BOND : angle 1.10883 ( 8) hydrogen bonds : bond 0.05030 ( 580) hydrogen bonds : angle 4.59727 ( 1680) link_BETA1-3 : bond 0.00402 ( 1) link_BETA1-3 : angle 2.23729 ( 3) link_BETA1-4 : bond 0.00553 ( 7) link_BETA1-4 : angle 1.94328 ( 21) link_BETA1-6 : bond 0.01521 ( 1) link_BETA1-6 : angle 2.81725 ( 3) link_NAG-ASN : bond 0.00579 ( 12) link_NAG-ASN : angle 3.77766 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7775 (mptp) REVERT: A 77 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7273 (mp0) REVERT: A 78 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7936 (ptpp) REVERT: A 81 ASP cc_start: 0.7451 (m-30) cc_final: 0.7220 (m-30) REVERT: A 206 SER cc_start: 0.7528 (m) cc_final: 0.7250 (p) REVERT: A 351 LYS cc_start: 0.7607 (mmtp) cc_final: 0.7297 (mtpp) REVERT: A 439 VAL cc_start: 0.7482 (t) cc_final: 0.7255 (p) REVERT: A 474 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 500 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6652 (tm-30) REVERT: A 512 GLN cc_start: 0.8042 (tt0) cc_final: 0.7701 (tt0) REVERT: A 543 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7017 (mtm110) REVERT: A 644 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: A 693 LYS cc_start: 0.7283 (mmtp) cc_final: 0.6537 (mtpp) REVERT: B 160 LYS cc_start: 0.7692 (mttm) cc_final: 0.6688 (mppt) REVERT: B 287 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7757 (tp) REVERT: B 380 LYS cc_start: 0.7714 (mtmm) cc_final: 0.7464 (mttp) REVERT: C 211 GLU cc_start: 0.7550 (pt0) cc_final: 0.7322 (pm20) REVERT: D 40 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7128 (mp0) REVERT: D 84 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7256 (mtt90) outliers start: 29 outliers final: 10 residues processed: 166 average time/residue: 0.4323 time to fit residues: 78.2300 Evaluate side-chains 131 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.175060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130059 restraints weight = 11951.413| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.16 r_work: 0.3185 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11244 Z= 0.137 Angle : 0.646 12.949 15359 Z= 0.307 Chirality : 0.043 0.338 1828 Planarity : 0.004 0.053 1848 Dihedral : 10.625 108.793 2104 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.60 % Allowed : 10.45 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.23), residues: 1322 helix: 1.14 (0.19), residues: 730 sheet: -1.22 (0.45), residues: 113 loop : -2.02 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 543 TYR 0.016 0.001 TYR C 218 PHE 0.037 0.002 PHE A 302 TRP 0.015 0.001 TRP D 74 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00312 (11219) covalent geometry : angle 0.61936 (15288) SS BOND : bond 0.00369 ( 4) SS BOND : angle 0.84482 ( 8) hydrogen bonds : bond 0.04394 ( 580) hydrogen bonds : angle 4.18566 ( 1680) link_BETA1-3 : bond 0.00816 ( 1) link_BETA1-3 : angle 1.36571 ( 3) link_BETA1-4 : bond 0.00644 ( 7) link_BETA1-4 : angle 1.91170 ( 21) link_BETA1-6 : bond 0.01633 ( 1) link_BETA1-6 : angle 3.26865 ( 3) link_NAG-ASN : bond 0.00755 ( 12) link_NAG-ASN : angle 3.45285 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7475 (pt0) cc_final: 0.7185 (mm-30) REVERT: A 46 LYS cc_start: 0.8070 (mmmm) cc_final: 0.7748 (mptp) REVERT: A 77 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7233 (mp0) REVERT: A 78 LYS cc_start: 0.8272 (ptpt) cc_final: 0.7841 (ptpp) REVERT: A 80 GLU cc_start: 0.7478 (tp30) cc_final: 0.7174 (mp0) REVERT: A 81 ASP cc_start: 0.7611 (m-30) cc_final: 0.7335 (m-30) REVERT: A 83 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7211 (mt0) REVERT: A 206 SER cc_start: 0.7569 (m) cc_final: 0.7294 (p) REVERT: A 296 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: A 317 ASP cc_start: 0.7556 (p0) cc_final: 0.7323 (p0) REVERT: A 351 LYS cc_start: 0.7640 (mmtp) cc_final: 0.7285 (mtpp) REVERT: A 364 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: A 469 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7273 (mp0) REVERT: A 474 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 500 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6310 (tt0) REVERT: A 512 GLN cc_start: 0.8011 (tt0) cc_final: 0.7644 (tt0) REVERT: A 543 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.6832 (mtm110) REVERT: A 644 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: A 693 LYS cc_start: 0.7433 (mmtp) cc_final: 0.6553 (mtpp) REVERT: B 80 LYS cc_start: 0.7508 (tppt) cc_final: 0.7013 (tptt) REVERT: B 160 LYS cc_start: 0.7642 (mttm) cc_final: 0.6639 (mppt) REVERT: B 380 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7655 (mttm) REVERT: C 211 GLU cc_start: 0.7679 (pt0) cc_final: 0.7430 (pm20) REVERT: D 40 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7234 (mp0) REVERT: D 84 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7258 (mtt90) outliers start: 41 outliers final: 15 residues processed: 168 average time/residue: 0.4162 time to fit residues: 76.7411 Evaluate side-chains 130 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 17 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 0.0000 chunk 59 optimal weight: 5.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.174473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127904 restraints weight = 11823.373| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.14 r_work: 0.3077 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11244 Z= 0.193 Angle : 0.722 13.301 15359 Z= 0.347 Chirality : 0.046 0.291 1828 Planarity : 0.005 0.050 1848 Dihedral : 10.265 94.097 2104 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.99 % Allowed : 12.91 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.23), residues: 1322 helix: 1.17 (0.19), residues: 736 sheet: -1.10 (0.46), residues: 117 loop : -1.94 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 619 TYR 0.018 0.002 TYR C 218 PHE 0.037 0.003 PHE A 302 TRP 0.022 0.002 TRP B 244 HIS 0.011 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00474 (11219) covalent geometry : angle 0.69600 (15288) SS BOND : bond 0.00561 ( 4) SS BOND : angle 0.94297 ( 8) hydrogen bonds : bond 0.04881 ( 580) hydrogen bonds : angle 4.23829 ( 1680) link_BETA1-3 : bond 0.00537 ( 1) link_BETA1-3 : angle 2.07869 ( 3) link_BETA1-4 : bond 0.00328 ( 7) link_BETA1-4 : angle 2.09121 ( 21) link_BETA1-6 : bond 0.01007 ( 1) link_BETA1-6 : angle 3.32692 ( 3) link_NAG-ASN : bond 0.00578 ( 12) link_NAG-ASN : angle 3.57047 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7515 (pt0) cc_final: 0.7063 (mm-30) REVERT: A 46 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7839 (mptp) REVERT: A 77 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7305 (mm-30) REVERT: A 78 LYS cc_start: 0.8363 (ptpt) cc_final: 0.7723 (ptpp) REVERT: A 80 GLU cc_start: 0.7518 (tp30) cc_final: 0.7273 (mp0) REVERT: A 81 ASP cc_start: 0.7747 (m-30) cc_final: 0.7487 (m-30) REVERT: A 83 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7325 (tt0) REVERT: A 206 SER cc_start: 0.7542 (m) cc_final: 0.7260 (p) REVERT: A 225 ILE cc_start: 0.8863 (mt) cc_final: 0.8524 (mm) REVERT: A 240 PHE cc_start: 0.7224 (m-10) cc_final: 0.7020 (m-10) REVERT: A 296 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: A 317 ASP cc_start: 0.7586 (p0) cc_final: 0.7359 (p0) REVERT: A 351 LYS cc_start: 0.7656 (mmtp) cc_final: 0.7283 (mtpp) REVERT: A 384 SER cc_start: 0.7389 (OUTLIER) cc_final: 0.6582 (m) REVERT: A 415 ARG cc_start: 0.7492 (ptp-170) cc_final: 0.7244 (ptp-170) REVERT: A 420 GLN cc_start: 0.8159 (pt0) cc_final: 0.7698 (pt0) REVERT: A 474 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 479 PHE cc_start: 0.7894 (t80) cc_final: 0.7532 (t80) REVERT: A 500 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6383 (tt0) REVERT: A 543 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.6843 (mtm180) REVERT: A 582 THR cc_start: 0.6453 (OUTLIER) cc_final: 0.6180 (p) REVERT: A 587 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7043 (mm110) REVERT: A 693 LYS cc_start: 0.7705 (mmtp) cc_final: 0.6775 (mtpp) REVERT: B 160 LYS cc_start: 0.7676 (mttm) cc_final: 0.6779 (mppt) REVERT: B 289 SER cc_start: 0.8493 (p) cc_final: 0.8222 (t) REVERT: D 40 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7418 (mp0) outliers start: 34 outliers final: 13 residues processed: 140 average time/residue: 0.5215 time to fit residues: 78.9952 Evaluate side-chains 128 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 118 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.170640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123878 restraints weight = 11831.397| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.11 r_work: 0.3095 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11244 Z= 0.146 Angle : 0.636 12.025 15359 Z= 0.304 Chirality : 0.043 0.285 1828 Planarity : 0.004 0.041 1848 Dihedral : 9.646 77.497 2104 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.81 % Allowed : 13.61 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1322 helix: 1.55 (0.20), residues: 735 sheet: -0.95 (0.47), residues: 116 loop : -1.78 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 84 TYR 0.014 0.001 TYR A 337 PHE 0.033 0.002 PHE A 302 TRP 0.013 0.001 TRP D 74 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00348 (11219) covalent geometry : angle 0.61296 (15288) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.81324 ( 8) hydrogen bonds : bond 0.04127 ( 580) hydrogen bonds : angle 4.05744 ( 1680) link_BETA1-3 : bond 0.00773 ( 1) link_BETA1-3 : angle 1.50509 ( 3) link_BETA1-4 : bond 0.00392 ( 7) link_BETA1-4 : angle 1.66651 ( 21) link_BETA1-6 : bond 0.01099 ( 1) link_BETA1-6 : angle 3.15577 ( 3) link_NAG-ASN : bond 0.00594 ( 12) link_NAG-ASN : angle 3.19756 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7501 (pt0) cc_final: 0.7076 (mm-30) REVERT: A 46 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7805 (mptp) REVERT: A 77 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7303 (mm-30) REVERT: A 78 LYS cc_start: 0.8379 (ptpt) cc_final: 0.7771 (ptpp) REVERT: A 81 ASP cc_start: 0.7773 (m-30) cc_final: 0.7500 (m-30) REVERT: A 139 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7982 (tp40) REVERT: A 155 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6555 (pm20) REVERT: A 206 SER cc_start: 0.7651 (m) cc_final: 0.7352 (p) REVERT: A 225 ILE cc_start: 0.8760 (mt) cc_final: 0.8425 (mm) REVERT: A 296 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: A 317 ASP cc_start: 0.7621 (p0) cc_final: 0.7364 (p0) REVERT: A 351 LYS cc_start: 0.7625 (mmtp) cc_final: 0.7293 (mtpp) REVERT: A 384 SER cc_start: 0.7525 (OUTLIER) cc_final: 0.6733 (m) REVERT: A 415 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.7262 (ptp-170) REVERT: A 420 GLN cc_start: 0.8161 (pt0) cc_final: 0.7703 (pt0) REVERT: A 474 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 479 PHE cc_start: 0.7944 (t80) cc_final: 0.7576 (t80) REVERT: A 500 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6171 (tt0) REVERT: A 543 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.6945 (mtm110) REVERT: A 587 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6926 (mm110) REVERT: A 644 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: A 693 LYS cc_start: 0.7739 (mmtp) cc_final: 0.6802 (mtpp) REVERT: B 146 MET cc_start: 0.6643 (mtm) cc_final: 0.6329 (ttm) REVERT: B 160 LYS cc_start: 0.7636 (mttm) cc_final: 0.6727 (mppt) REVERT: B 289 SER cc_start: 0.8499 (p) cc_final: 0.8235 (t) REVERT: D 40 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7406 (mp0) REVERT: D 84 ARG cc_start: 0.7559 (mtt90) cc_final: 0.6887 (mtt90) outliers start: 32 outliers final: 14 residues processed: 144 average time/residue: 0.4911 time to fit residues: 76.4238 Evaluate side-chains 129 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.175691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129906 restraints weight = 11839.086| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.15 r_work: 0.3081 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11244 Z= 0.150 Angle : 0.641 12.412 15359 Z= 0.305 Chirality : 0.043 0.282 1828 Planarity : 0.004 0.042 1848 Dihedral : 8.957 70.473 2104 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.78 % Allowed : 14.40 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.24), residues: 1322 helix: 1.69 (0.20), residues: 736 sheet: -0.86 (0.48), residues: 116 loop : -1.74 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 84 TYR 0.014 0.001 TYR A 337 PHE 0.033 0.002 PHE A 302 TRP 0.011 0.001 TRP B 244 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00360 (11219) covalent geometry : angle 0.61892 (15288) SS BOND : bond 0.00307 ( 4) SS BOND : angle 0.65005 ( 8) hydrogen bonds : bond 0.04123 ( 580) hydrogen bonds : angle 4.02505 ( 1680) link_BETA1-3 : bond 0.00651 ( 1) link_BETA1-3 : angle 1.27560 ( 3) link_BETA1-4 : bond 0.00319 ( 7) link_BETA1-4 : angle 1.63281 ( 21) link_BETA1-6 : bond 0.00860 ( 1) link_BETA1-6 : angle 3.25683 ( 3) link_NAG-ASN : bond 0.00568 ( 12) link_NAG-ASN : angle 3.17133 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7534 (pt0) cc_final: 0.7097 (mm-30) REVERT: A 46 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7821 (mptp) REVERT: A 77 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7311 (mm-30) REVERT: A 78 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7740 (ptpp) REVERT: A 81 ASP cc_start: 0.7838 (m-30) cc_final: 0.7572 (m-30) REVERT: A 139 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8011 (tp40) REVERT: A 225 ILE cc_start: 0.8799 (mt) cc_final: 0.8484 (mm) REVERT: A 283 ASP cc_start: 0.8106 (p0) cc_final: 0.7780 (p0) REVERT: A 296 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: A 317 ASP cc_start: 0.7532 (p0) cc_final: 0.7261 (p0) REVERT: A 351 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7314 (mtpp) REVERT: A 384 SER cc_start: 0.7510 (OUTLIER) cc_final: 0.6739 (m) REVERT: A 415 ARG cc_start: 0.7522 (ptp-170) cc_final: 0.7257 (ptp-170) REVERT: A 420 GLN cc_start: 0.8126 (pt0) cc_final: 0.7692 (pt0) REVERT: A 474 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7206 (mm-30) REVERT: A 500 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6213 (tt0) REVERT: A 543 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.6838 (mtm180) REVERT: A 582 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.6088 (p) REVERT: A 587 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7006 (mm110) REVERT: A 644 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: A 693 LYS cc_start: 0.7798 (mmtp) cc_final: 0.6847 (mtpp) REVERT: B 160 LYS cc_start: 0.7640 (mttm) cc_final: 0.6715 (mppt) REVERT: B 289 SER cc_start: 0.8500 (p) cc_final: 0.8236 (t) REVERT: D 40 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7425 (mp0) outliers start: 43 outliers final: 20 residues processed: 148 average time/residue: 0.5308 time to fit residues: 84.8504 Evaluate side-chains 136 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 512 GLN B 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.171795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125216 restraints weight = 11868.052| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.17 r_work: 0.3160 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11244 Z= 0.176 Angle : 0.664 12.386 15359 Z= 0.317 Chirality : 0.044 0.276 1828 Planarity : 0.004 0.041 1848 Dihedral : 8.704 66.638 2104 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.78 % Allowed : 14.49 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1322 helix: 1.59 (0.19), residues: 741 sheet: -0.81 (0.48), residues: 115 loop : -1.71 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 84 TYR 0.014 0.001 TYR A 337 PHE 0.034 0.002 PHE A 302 TRP 0.011 0.001 TRP B 244 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00433 (11219) covalent geometry : angle 0.64326 (15288) SS BOND : bond 0.00364 ( 4) SS BOND : angle 0.69565 ( 8) hydrogen bonds : bond 0.04370 ( 580) hydrogen bonds : angle 4.06827 ( 1680) link_BETA1-3 : bond 0.00639 ( 1) link_BETA1-3 : angle 1.39090 ( 3) link_BETA1-4 : bond 0.00254 ( 7) link_BETA1-4 : angle 1.65812 ( 21) link_BETA1-6 : bond 0.00916 ( 1) link_BETA1-6 : angle 3.11628 ( 3) link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 3.10399 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8255 (mmmm) cc_final: 0.7876 (mptp) REVERT: A 77 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7342 (mm-30) REVERT: A 78 LYS cc_start: 0.8312 (ptpt) cc_final: 0.7736 (ptpp) REVERT: A 81 ASP cc_start: 0.7926 (m-30) cc_final: 0.7665 (m-30) REVERT: A 139 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8098 (tp40) REVERT: A 225 ILE cc_start: 0.8823 (mt) cc_final: 0.8521 (mm) REVERT: A 296 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: A 317 ASP cc_start: 0.7584 (p0) cc_final: 0.7293 (p0) REVERT: A 351 LYS cc_start: 0.7785 (mmtp) cc_final: 0.7374 (mtpp) REVERT: A 364 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: A 384 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.6828 (m) REVERT: A 415 ARG cc_start: 0.7543 (ptp-170) cc_final: 0.7280 (ptp-170) REVERT: A 420 GLN cc_start: 0.8123 (pt0) cc_final: 0.7703 (pt0) REVERT: A 474 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 500 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6234 (tt0) REVERT: A 543 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.6969 (mtm180) REVERT: A 587 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7064 (mm110) REVERT: A 644 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: A 693 LYS cc_start: 0.7818 (mmtp) cc_final: 0.6859 (mtpp) REVERT: B 160 LYS cc_start: 0.7706 (mttm) cc_final: 0.6814 (mppt) REVERT: C 82 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6914 (mt) REVERT: D 40 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7484 (mp0) outliers start: 43 outliers final: 23 residues processed: 147 average time/residue: 0.5035 time to fit residues: 80.2730 Evaluate side-chains 140 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.173909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127729 restraints weight = 11884.801| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.14 r_work: 0.3127 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11244 Z= 0.110 Angle : 0.582 11.199 15359 Z= 0.277 Chirality : 0.042 0.278 1828 Planarity : 0.004 0.041 1848 Dihedral : 8.006 65.647 2104 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.19 % Allowed : 16.24 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.24), residues: 1322 helix: 1.97 (0.20), residues: 736 sheet: -0.85 (0.46), residues: 125 loop : -1.63 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 84 TYR 0.011 0.001 TYR A 337 PHE 0.029 0.001 PHE A 302 TRP 0.011 0.001 TRP D 74 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00248 (11219) covalent geometry : angle 0.56162 (15288) SS BOND : bond 0.00409 ( 4) SS BOND : angle 0.74149 ( 8) hydrogen bonds : bond 0.03473 ( 580) hydrogen bonds : angle 3.90872 ( 1680) link_BETA1-3 : bond 0.00688 ( 1) link_BETA1-3 : angle 1.21260 ( 3) link_BETA1-4 : bond 0.00337 ( 7) link_BETA1-4 : angle 1.45738 ( 21) link_BETA1-6 : bond 0.00890 ( 1) link_BETA1-6 : angle 2.88168 ( 3) link_NAG-ASN : bond 0.00542 ( 12) link_NAG-ASN : angle 2.88293 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7506 (pt0) cc_final: 0.7078 (mm-30) REVERT: A 46 LYS cc_start: 0.8151 (mmmm) cc_final: 0.7706 (mptp) REVERT: A 77 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7252 (mm-30) REVERT: A 78 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7594 (ptpp) REVERT: A 81 ASP cc_start: 0.7778 (m-30) cc_final: 0.7517 (m-30) REVERT: A 139 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7911 (tp40) REVERT: A 225 ILE cc_start: 0.8703 (mt) cc_final: 0.8419 (mm) REVERT: A 283 ASP cc_start: 0.8009 (p0) cc_final: 0.7726 (p0) REVERT: A 317 ASP cc_start: 0.7437 (p0) cc_final: 0.7173 (p0) REVERT: A 343 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.6707 (tpt) REVERT: A 351 LYS cc_start: 0.7698 (mmtp) cc_final: 0.7306 (mtpp) REVERT: A 384 SER cc_start: 0.7477 (OUTLIER) cc_final: 0.6748 (m) REVERT: A 415 ARG cc_start: 0.7438 (ptp-170) cc_final: 0.7172 (ptp-170) REVERT: A 420 GLN cc_start: 0.8052 (pt0) cc_final: 0.7641 (pt0) REVERT: A 474 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 500 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6187 (tt0) REVERT: A 543 ARG cc_start: 0.7169 (mtm-85) cc_final: 0.6767 (mtm110) REVERT: A 582 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6140 (p) REVERT: A 619 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6291 (ptt90) REVERT: A 670 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7209 (mp) REVERT: B 160 LYS cc_start: 0.7619 (mttm) cc_final: 0.6703 (mppt) REVERT: D 40 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7460 (mp0) REVERT: D 84 ARG cc_start: 0.7420 (mtt90) cc_final: 0.7193 (mtt90) outliers start: 25 outliers final: 10 residues processed: 134 average time/residue: 0.5146 time to fit residues: 74.7781 Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 512 GLN B 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.171268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124038 restraints weight = 11866.524| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.24 r_work: 0.3180 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11244 Z= 0.149 Angle : 0.626 11.718 15359 Z= 0.298 Chirality : 0.043 0.277 1828 Planarity : 0.004 0.041 1848 Dihedral : 7.816 63.545 2104 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.19 % Allowed : 15.63 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.24), residues: 1322 helix: 1.82 (0.20), residues: 744 sheet: -0.76 (0.46), residues: 127 loop : -1.57 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 84 TYR 0.014 0.001 TYR A 337 PHE 0.032 0.002 PHE A 302 TRP 0.011 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00361 (11219) covalent geometry : angle 0.60648 (15288) SS BOND : bond 0.00383 ( 4) SS BOND : angle 0.80362 ( 8) hydrogen bonds : bond 0.03966 ( 580) hydrogen bonds : angle 3.94301 ( 1680) link_BETA1-3 : bond 0.00696 ( 1) link_BETA1-3 : angle 1.36920 ( 3) link_BETA1-4 : bond 0.00259 ( 7) link_BETA1-4 : angle 1.58572 ( 21) link_BETA1-6 : bond 0.01016 ( 1) link_BETA1-6 : angle 2.70602 ( 3) link_NAG-ASN : bond 0.00513 ( 12) link_NAG-ASN : angle 2.93722 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7583 (pt0) cc_final: 0.7177 (mm-30) REVERT: A 46 LYS cc_start: 0.8320 (mmmm) cc_final: 0.7792 (mptp) REVERT: A 77 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7348 (mm-30) REVERT: A 78 LYS cc_start: 0.8292 (ptpt) cc_final: 0.7680 (ptpp) REVERT: A 81 ASP cc_start: 0.7893 (m-30) cc_final: 0.7619 (m-30) REVERT: A 139 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8062 (tp40) REVERT: A 225 ILE cc_start: 0.8788 (mt) cc_final: 0.8524 (mm) REVERT: A 283 ASP cc_start: 0.8066 (p0) cc_final: 0.7783 (p0) REVERT: A 317 ASP cc_start: 0.7500 (p0) cc_final: 0.7186 (p0) REVERT: A 343 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.6910 (tpt) REVERT: A 351 LYS cc_start: 0.7630 (mmtp) cc_final: 0.7219 (mtpp) REVERT: A 384 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.6858 (m) REVERT: A 415 ARG cc_start: 0.7496 (ptp-170) cc_final: 0.7231 (ptp-170) REVERT: A 420 GLN cc_start: 0.8106 (pt0) cc_final: 0.7678 (pt0) REVERT: A 474 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 500 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6261 (tt0) REVERT: A 543 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.6926 (mtm180) REVERT: A 619 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6434 (ptt90) REVERT: A 670 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7164 (mp) REVERT: B 160 LYS cc_start: 0.7671 (mttm) cc_final: 0.6758 (mppt) REVERT: C 82 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6940 (mt) REVERT: D 40 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7603 (mp0) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 0.5756 time to fit residues: 82.7270 Evaluate side-chains 130 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 3.9990 chunk 37 optimal weight: 0.0570 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.168236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121777 restraints weight = 11908.388| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.11 r_work: 0.3178 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11244 Z= 0.166 Angle : 0.652 12.265 15359 Z= 0.311 Chirality : 0.044 0.270 1828 Planarity : 0.004 0.042 1848 Dihedral : 7.650 60.297 2104 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 2.46 % Allowed : 15.45 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1322 helix: 1.68 (0.19), residues: 745 sheet: -0.76 (0.47), residues: 125 loop : -1.59 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 84 TYR 0.014 0.001 TYR A 337 PHE 0.033 0.002 PHE A 302 TRP 0.012 0.001 TRP C 209 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00407 (11219) covalent geometry : angle 0.63287 (15288) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.78875 ( 8) hydrogen bonds : bond 0.04213 ( 580) hydrogen bonds : angle 4.02002 ( 1680) link_BETA1-3 : bond 0.00610 ( 1) link_BETA1-3 : angle 1.38326 ( 3) link_BETA1-4 : bond 0.00225 ( 7) link_BETA1-4 : angle 1.64984 ( 21) link_BETA1-6 : bond 0.00853 ( 1) link_BETA1-6 : angle 2.19785 ( 3) link_NAG-ASN : bond 0.00541 ( 12) link_NAG-ASN : angle 2.99998 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7755 (pt0) cc_final: 0.7242 (mm-30) REVERT: A 46 LYS cc_start: 0.8303 (mmmm) cc_final: 0.7749 (mptp) REVERT: A 77 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7404 (mm-30) REVERT: A 78 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7541 (ptpp) REVERT: A 81 ASP cc_start: 0.7927 (m-30) cc_final: 0.7655 (m-30) REVERT: A 139 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8147 (tp40) REVERT: A 225 ILE cc_start: 0.8846 (mt) cc_final: 0.8575 (mm) REVERT: A 270 LYS cc_start: 0.6916 (mttm) cc_final: 0.6583 (mtpp) REVERT: A 283 ASP cc_start: 0.8258 (p0) cc_final: 0.7967 (p0) REVERT: A 317 ASP cc_start: 0.7414 (p0) cc_final: 0.7130 (p0) REVERT: A 343 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7106 (tpt) REVERT: A 351 LYS cc_start: 0.7679 (mmtp) cc_final: 0.7258 (mtpp) REVERT: A 384 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.6699 (m) REVERT: A 415 ARG cc_start: 0.7488 (ptp-170) cc_final: 0.7181 (ptp-170) REVERT: A 420 GLN cc_start: 0.8071 (pt0) cc_final: 0.7658 (pt0) REVERT: A 474 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 500 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6250 (tt0) REVERT: A 543 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7076 (mtm180) REVERT: A 619 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6415 (ptt90) REVERT: A 693 LYS cc_start: 0.7920 (mmtp) cc_final: 0.7006 (mtpp) REVERT: B 160 LYS cc_start: 0.7685 (mttm) cc_final: 0.6773 (mppt) REVERT: B 189 TYR cc_start: 0.7855 (m-10) cc_final: 0.7406 (m-80) REVERT: C 82 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7159 (mt) REVERT: D 40 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7552 (mp0) outliers start: 28 outliers final: 14 residues processed: 135 average time/residue: 0.5389 time to fit residues: 78.9455 Evaluate side-chains 127 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 512 GLN B 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.168590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122449 restraints weight = 11873.232| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.08 r_work: 0.3193 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11244 Z= 0.167 Angle : 0.649 11.730 15359 Z= 0.310 Chirality : 0.044 0.269 1828 Planarity : 0.004 0.043 1848 Dihedral : 7.526 58.200 2104 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 2.02 % Allowed : 15.80 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.24), residues: 1322 helix: 1.68 (0.19), residues: 744 sheet: -0.77 (0.47), residues: 127 loop : -1.55 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 84 TYR 0.014 0.001 TYR A 337 PHE 0.033 0.002 PHE A 302 TRP 0.012 0.001 TRP C 209 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00410 (11219) covalent geometry : angle 0.63025 (15288) SS BOND : bond 0.00380 ( 4) SS BOND : angle 0.76227 ( 8) hydrogen bonds : bond 0.04212 ( 580) hydrogen bonds : angle 4.01859 ( 1680) link_BETA1-3 : bond 0.00606 ( 1) link_BETA1-3 : angle 1.38882 ( 3) link_BETA1-4 : bond 0.00231 ( 7) link_BETA1-4 : angle 1.65504 ( 21) link_BETA1-6 : bond 0.00843 ( 1) link_BETA1-6 : angle 1.77020 ( 3) link_NAG-ASN : bond 0.00531 ( 12) link_NAG-ASN : angle 2.93377 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.03 seconds wall clock time: 50 minutes 8.48 seconds (3008.48 seconds total)