Starting phenix.real_space_refine on Fri Jan 17 14:21:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x53_38060/01_2025/8x53_38060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x53_38060/01_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_38060/01_2025/8x53_38060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x53_38060/01_2025/8x53_38060.map" model { file = "/net/cci-nas-00/data/ceres_data/8x53_38060/01_2025/8x53_38060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x53_38060/01_2025/8x53_38060.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.44, per 1000 atoms: 0.59 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.01 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: 3.27 Time building geometry restraints manager: 3.26 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: 0.360 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 26.180 Find NCS groups from input model: 0.130 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.710 ------------------------------------------------------------------------------- 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 : 0.010 0.224 11219 Z= 0.652 Angle : 1.212 28.633 15288 Z= 0.731 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (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 TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 PHE 0.060 0.003 PHE B 386 TYR 0.035 0.003 TYR A 565 ARG 0.009 0.001 ARG A 626 *********************** 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 : 1.097 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: 1.0854 time to fit residues: 252.0288 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 : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.180677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136481 restraints weight = 11821.896| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.05 r_work: 0.3287 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11219 Z= 0.181 Angle : 0.662 13.493 15288 Z= 0.327 Chirality : 0.044 0.343 1828 Planarity : 0.005 0.068 1848 Dihedral : 12.870 103.416 2104 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.46 % Allowed : 7.90 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1322 helix: 0.28 (0.19), residues: 731 sheet: -1.17 (0.48), residues: 108 loop : -2.32 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 227 HIS 0.010 0.001 HIS C 197 PHE 0.035 0.002 PHE A 302 TYR 0.014 0.001 TYR A 565 ARG 0.004 0.000 ARG A 626 *********************** 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 177 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7775 (mptp) REVERT: A 77 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7259 (mp0) REVERT: A 78 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7873 (ptpp) REVERT: A 81 ASP cc_start: 0.7419 (m-30) cc_final: 0.7182 (m-30) REVERT: A 161 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6865 (tp30) REVERT: A 206 SER cc_start: 0.7530 (m) cc_final: 0.7256 (p) REVERT: A 351 LYS cc_start: 0.7614 (mmtp) cc_final: 0.7310 (mtpp) REVERT: A 439 VAL cc_start: 0.7471 (t) cc_final: 0.7245 (p) REVERT: A 474 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 500 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6648 (tm-30) REVERT: A 512 GLN cc_start: 0.7977 (tt0) cc_final: 0.7631 (tt0) REVERT: A 543 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.6809 (mtm110) REVERT: A 644 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: A 693 LYS cc_start: 0.7278 (mmtp) cc_final: 0.6537 (mtpp) REVERT: B 160 LYS cc_start: 0.7689 (mttm) cc_final: 0.6680 (mppt) REVERT: B 287 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7752 (tp) REVERT: B 380 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7379 (mttp) REVERT: C 211 GLU cc_start: 0.7583 (pt0) cc_final: 0.7341 (pm20) REVERT: D 40 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7112 (mp0) REVERT: D 84 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7259 (mtt90) outliers start: 28 outliers final: 9 residues processed: 168 average time/residue: 1.1222 time to fit residues: 205.9421 Evaluate side-chains 129 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 E residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 305 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.167553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119772 restraints weight = 11990.323| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.18 r_work: 0.3074 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11219 Z= 0.375 Angle : 0.756 13.868 15288 Z= 0.370 Chirality : 0.048 0.342 1828 Planarity : 0.005 0.062 1848 Dihedral : 11.045 105.717 2104 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.69 % Allowed : 11.15 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1322 helix: 0.80 (0.19), residues: 724 sheet: -1.47 (0.44), residues: 114 loop : -2.12 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 640 HIS 0.014 0.002 HIS C 197 PHE 0.042 0.003 PHE A 302 TYR 0.025 0.002 TYR C 218 ARG 0.006 0.001 ARG A 233 *********************** 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 167 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7516 (pt0) cc_final: 0.7081 (mm-30) REVERT: A 46 LYS cc_start: 0.8339 (mmmm) cc_final: 0.7962 (mptp) REVERT: A 77 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7169 (mm-30) REVERT: A 78 LYS cc_start: 0.8387 (ptpt) cc_final: 0.7790 (ptpp) REVERT: A 80 GLU cc_start: 0.7503 (tp30) cc_final: 0.7225 (mp0) REVERT: A 81 ASP cc_start: 0.7592 (m-30) cc_final: 0.7350 (m-30) REVERT: A 83 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7243 (tt0) REVERT: A 139 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7986 (tp40) REVERT: A 206 SER cc_start: 0.7546 (m) cc_final: 0.7268 (p) REVERT: A 296 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A 317 ASP cc_start: 0.7608 (p0) cc_final: 0.7400 (p0) REVERT: A 351 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7329 (mtpp) REVERT: A 364 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: A 367 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8489 (mt0) REVERT: A 384 SER cc_start: 0.7343 (OUTLIER) cc_final: 0.6567 (m) REVERT: A 415 ARG cc_start: 0.7532 (ptp-170) cc_final: 0.7173 (ptp-170) REVERT: A 469 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7202 (mp0) REVERT: A 474 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 500 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6405 (tt0) REVERT: A 512 GLN cc_start: 0.8075 (tt0) cc_final: 0.7705 (tt0) REVERT: A 543 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.6863 (mtm110) REVERT: A 644 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 693 LYS cc_start: 0.7636 (mmtp) cc_final: 0.6718 (mtpp) REVERT: B 160 LYS cc_start: 0.7728 (mttm) cc_final: 0.6780 (mppt) REVERT: B 289 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8227 (t) REVERT: D 40 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7325 (mp0) outliers start: 42 outliers final: 16 residues processed: 155 average time/residue: 1.1482 time to fit residues: 193.7114 Evaluate side-chains 132 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER 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 343 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 367 GLN 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 586 CYS 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 289 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 82 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.167239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119539 restraints weight = 11860.182| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.19 r_work: 0.3047 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11219 Z= 0.328 Angle : 0.687 13.257 15288 Z= 0.339 Chirality : 0.046 0.286 1828 Planarity : 0.004 0.046 1848 Dihedral : 10.447 93.698 2104 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.42 % Allowed : 12.64 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1322 helix: 1.10 (0.19), residues: 732 sheet: -1.05 (0.47), residues: 115 loop : -1.99 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 244 HIS 0.011 0.002 HIS C 197 PHE 0.039 0.002 PHE A 302 TYR 0.014 0.002 TYR A 337 ARG 0.006 0.001 ARG D 84 *********************** 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 160 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7618 (pt0) cc_final: 0.7156 (mm-30) REVERT: A 46 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7907 (mptp) REVERT: A 77 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7344 (mm-30) REVERT: A 78 LYS cc_start: 0.8286 (ptpt) cc_final: 0.7711 (ptpp) REVERT: A 80 GLU cc_start: 0.7632 (tp30) cc_final: 0.7389 (mp0) REVERT: A 81 ASP cc_start: 0.7784 (m-30) cc_final: 0.7548 (m-30) REVERT: A 83 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7370 (tt0) REVERT: A 114 ARG cc_start: 0.6614 (mtt-85) cc_final: 0.6390 (mtp85) REVERT: A 139 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8080 (tp40) REVERT: A 296 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: A 317 ASP cc_start: 0.7642 (p0) cc_final: 0.7374 (p0) REVERT: A 351 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7307 (mtpp) REVERT: A 415 ARG cc_start: 0.7535 (ptp-170) cc_final: 0.7220 (ptp-170) REVERT: A 474 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 500 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6290 (tt0) REVERT: A 543 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.6960 (mtm180) REVERT: A 587 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7027 (mm110) REVERT: A 644 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: A 693 LYS cc_start: 0.7738 (mmtp) cc_final: 0.6776 (mtpp) REVERT: B 160 LYS cc_start: 0.7651 (mttm) cc_final: 0.6734 (mppt) REVERT: B 210 MET cc_start: 0.8363 (tpp) cc_final: 0.8123 (mmp) REVERT: B 289 SER cc_start: 0.8514 (p) cc_final: 0.8278 (t) REVERT: D 40 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7381 (mp0) outliers start: 39 outliers final: 20 residues processed: 151 average time/residue: 1.2985 time to fit residues: 212.1972 Evaluate side-chains 135 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER 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 561 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 140 ILE Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 287 ILE 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 72 THR Chi-restraints excluded: chain D residue 77 ILE 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 97 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 9 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 367 GLN A 512 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.169765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122506 restraints weight = 11784.191| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.17 r_work: 0.3077 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11219 Z= 0.211 Angle : 0.607 12.196 15288 Z= 0.297 Chirality : 0.043 0.292 1828 Planarity : 0.004 0.047 1848 Dihedral : 9.765 78.774 2104 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.16 % Allowed : 13.70 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1322 helix: 1.56 (0.20), residues: 733 sheet: -0.93 (0.48), residues: 115 loop : -1.87 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 74 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.014 0.001 TYR A 337 ARG 0.007 0.000 ARG D 84 *********************** 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 147 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7579 (pt0) cc_final: 0.7120 (mm-30) REVERT: A 46 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7812 (mptp) REVERT: A 77 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7294 (mm-30) REVERT: A 78 LYS cc_start: 0.8264 (ptpt) cc_final: 0.7700 (ptpp) REVERT: A 81 ASP cc_start: 0.7800 (m-30) cc_final: 0.7518 (m-30) REVERT: A 83 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7359 (tt0) REVERT: A 114 ARG cc_start: 0.6563 (mtt-85) cc_final: 0.6009 (mtp85) REVERT: A 118 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 139 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7990 (tp40) REVERT: A 317 ASP cc_start: 0.7616 (p0) cc_final: 0.7351 (p0) REVERT: A 351 LYS cc_start: 0.7748 (mmtp) cc_final: 0.7317 (mtpp) REVERT: A 364 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: A 384 SER cc_start: 0.7539 (OUTLIER) cc_final: 0.6725 (m) REVERT: A 415 ARG cc_start: 0.7479 (ptp-170) cc_final: 0.7174 (ptp-170) REVERT: A 474 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 500 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6195 (tt0) REVERT: A 543 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.6945 (mtm180) REVERT: A 582 THR cc_start: 0.6409 (OUTLIER) cc_final: 0.6137 (p) REVERT: A 587 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6926 (mm110) REVERT: A 638 SER cc_start: 0.8421 (m) cc_final: 0.8057 (t) REVERT: A 644 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: A 670 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7268 (mp) REVERT: A 693 LYS cc_start: 0.7774 (mmtp) cc_final: 0.6799 (mtpp) REVERT: B 93 MET cc_start: 0.8704 (mtm) cc_final: 0.8454 (mtm) REVERT: B 160 LYS cc_start: 0.7665 (mttm) cc_final: 0.6722 (mppt) REVERT: B 289 SER cc_start: 0.8513 (p) cc_final: 0.8267 (t) REVERT: D 40 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7419 (mp0) outliers start: 36 outliers final: 15 residues processed: 141 average time/residue: 1.2353 time to fit residues: 188.6276 Evaluate side-chains 128 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 118 ILE 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 364 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 670 LEU 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 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 77 ILE 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 95 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.169286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122061 restraints weight = 11985.987| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.16 r_work: 0.3063 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11219 Z= 0.256 Angle : 0.634 12.764 15288 Z= 0.309 Chirality : 0.044 0.282 1828 Planarity : 0.004 0.040 1848 Dihedral : 9.300 68.271 2104 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.21 % Allowed : 13.35 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1322 helix: 1.62 (0.20), residues: 733 sheet: -0.86 (0.48), residues: 115 loop : -1.80 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.007 0.001 HIS C 197 PHE 0.033 0.002 PHE A 302 TYR 0.015 0.001 TYR A 337 ARG 0.006 0.000 ARG D 84 *********************** 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 165 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7551 (pt0) cc_final: 0.7083 (mm-30) REVERT: A 46 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7800 (mptp) REVERT: A 77 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7292 (mm-30) REVERT: A 78 LYS cc_start: 0.8233 (ptpt) cc_final: 0.7657 (ptpp) REVERT: A 81 ASP cc_start: 0.7802 (m-30) cc_final: 0.7523 (m-30) REVERT: A 83 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7277 (tt0) REVERT: A 114 ARG cc_start: 0.6528 (mtt-85) cc_final: 0.6281 (mtp85) REVERT: A 139 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7944 (tp40) REVERT: A 296 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: A 317 ASP cc_start: 0.7557 (p0) cc_final: 0.7325 (p0) REVERT: A 351 LYS cc_start: 0.7712 (mmtp) cc_final: 0.7297 (mtpp) REVERT: A 384 SER cc_start: 0.7488 (OUTLIER) cc_final: 0.6618 (m) REVERT: A 474 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7228 (mm-30) REVERT: A 500 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6199 (tt0) REVERT: A 543 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6890 (mtm180) REVERT: A 582 THR cc_start: 0.6344 (OUTLIER) cc_final: 0.6071 (p) REVERT: A 638 SER cc_start: 0.8464 (m) cc_final: 0.8084 (t) REVERT: A 644 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: A 670 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7224 (mp) REVERT: B 160 LYS cc_start: 0.7661 (mttm) cc_final: 0.6717 (mppt) REVERT: D 40 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7428 (mp0) outliers start: 48 outliers final: 22 residues processed: 156 average time/residue: 1.2006 time to fit residues: 204.0723 Evaluate side-chains 136 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 SER 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 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 A residue 670 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 LEU 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 71 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 77 ILE 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 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.166212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119204 restraints weight = 12046.278| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.17 r_work: 0.3130 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11219 Z= 0.307 Angle : 0.660 12.955 15288 Z= 0.322 Chirality : 0.045 0.278 1828 Planarity : 0.004 0.044 1848 Dihedral : 9.114 64.589 2104 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.86 % Allowed : 13.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1322 helix: 1.52 (0.20), residues: 740 sheet: -0.87 (0.48), residues: 115 loop : -1.78 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.008 0.001 HIS C 197 PHE 0.034 0.002 PHE A 302 TYR 0.015 0.002 TYR A 337 ARG 0.006 0.000 ARG D 84 *********************** 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: 44 poor density : 114 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7616 (pt0) cc_final: 0.7200 (mm-30) REVERT: A 46 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7896 (mptp) REVERT: A 77 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7402 (mm-30) REVERT: A 78 LYS cc_start: 0.8344 (ptpt) cc_final: 0.7731 (ptpp) REVERT: A 81 ASP cc_start: 0.7898 (m-30) cc_final: 0.7657 (m-30) REVERT: A 114 ARG cc_start: 0.6594 (mtt-85) cc_final: 0.6354 (mtp85) REVERT: A 139 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8096 (tp40) REVERT: A 296 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: A 317 ASP cc_start: 0.7580 (p0) cc_final: 0.7304 (p0) REVERT: A 351 LYS cc_start: 0.7655 (mmtp) cc_final: 0.7248 (mtpp) REVERT: A 384 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.6832 (m) REVERT: A 474 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 500 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6257 (tt0) REVERT: A 543 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.7017 (mtm180) REVERT: A 638 SER cc_start: 0.8482 (m) cc_final: 0.8163 (t) REVERT: A 644 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: A 670 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7367 (mp) REVERT: B 160 LYS cc_start: 0.7715 (mttm) cc_final: 0.6824 (mppt) REVERT: C 82 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6956 (mt) REVERT: D 40 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7535 (mp0) outliers start: 44 outliers final: 25 residues processed: 147 average time/residue: 1.2312 time to fit residues: 196.2585 Evaluate side-chains 142 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 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 541 ASP 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 A residue 656 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 287 ILE 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 71 LEU Chi-restraints excluded: chain C residue 78 VAL 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 D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.168383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.121026 restraints weight = 11859.690| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.16 r_work: 0.3153 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11219 Z= 0.222 Angle : 0.609 12.261 15288 Z= 0.297 Chirality : 0.043 0.276 1828 Planarity : 0.004 0.042 1848 Dihedral : 8.663 62.710 2104 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 3.16 % Allowed : 14.93 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1322 helix: 1.74 (0.20), residues: 740 sheet: -0.85 (0.48), residues: 115 loop : -1.68 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.014 0.001 TYR A 337 ARG 0.006 0.000 ARG D 84 *********************** 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 150 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7618 (pt0) cc_final: 0.7229 (mm-30) REVERT: A 46 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7874 (mptp) REVERT: A 77 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7393 (mm-30) REVERT: A 78 LYS cc_start: 0.8328 (ptpt) cc_final: 0.7731 (ptpp) REVERT: A 81 ASP cc_start: 0.7937 (m-30) cc_final: 0.7718 (m-30) REVERT: A 114 ARG cc_start: 0.6667 (mtt-85) cc_final: 0.6307 (mtp85) REVERT: A 139 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8139 (tp40) REVERT: A 283 ASP cc_start: 0.8125 (p0) cc_final: 0.7806 (p0) REVERT: A 296 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 317 ASP cc_start: 0.7602 (p0) cc_final: 0.7340 (p0) REVERT: A 351 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7270 (mtpp) REVERT: A 384 SER cc_start: 0.7646 (OUTLIER) cc_final: 0.6852 (m) REVERT: A 420 GLN cc_start: 0.8141 (pt0) cc_final: 0.7697 (pt0) REVERT: A 474 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7195 (mm-30) REVERT: A 500 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6262 (tt0) REVERT: A 543 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.7031 (mtm180) REVERT: A 619 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6487 (ptt90) REVERT: B 160 LYS cc_start: 0.7693 (mttm) cc_final: 0.6811 (mppt) REVERT: C 82 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6962 (mt) REVERT: D 40 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7539 (mp0) outliers start: 36 outliers final: 21 residues processed: 143 average time/residue: 1.1911 time to fit residues: 184.8758 Evaluate side-chains 135 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 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 619 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 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 78 VAL 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 D residue 72 THR 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 109 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.182859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138628 restraints weight = 11738.639| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.12 r_work: 0.3144 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11219 Z= 0.152 Angle : 0.560 11.405 15288 Z= 0.272 Chirality : 0.042 0.282 1828 Planarity : 0.004 0.042 1848 Dihedral : 8.063 61.708 2104 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 2.11 % Allowed : 15.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1322 helix: 2.04 (0.20), residues: 737 sheet: -0.85 (0.46), residues: 125 loop : -1.58 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.004 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.012 0.001 TYR A 337 ARG 0.007 0.000 ARG D 84 *********************** 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 143 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7643 (pt0) cc_final: 0.7033 (mm-30) REVERT: A 46 LYS cc_start: 0.8070 (mmmm) cc_final: 0.7568 (mptp) REVERT: A 77 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7280 (mm-30) REVERT: A 78 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7376 (ptpp) REVERT: A 81 ASP cc_start: 0.7705 (m-30) cc_final: 0.7472 (m-30) REVERT: A 114 ARG cc_start: 0.6523 (mtt-85) cc_final: 0.6057 (mtp85) REVERT: A 139 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: A 283 ASP cc_start: 0.8107 (p0) cc_final: 0.7848 (p0) REVERT: A 317 ASP cc_start: 0.7309 (p0) cc_final: 0.7058 (p0) REVERT: A 351 LYS cc_start: 0.7474 (mmtp) cc_final: 0.7024 (mtpp) REVERT: A 364 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7851 (tp30) REVERT: A 384 SER cc_start: 0.7298 (OUTLIER) cc_final: 0.6585 (m) REVERT: A 420 GLN cc_start: 0.8006 (pt0) cc_final: 0.7596 (pt0) REVERT: A 474 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 500 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6103 (tt0) REVERT: A 543 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6861 (mtm110) REVERT: B 160 LYS cc_start: 0.7584 (mttm) cc_final: 0.6633 (mppt) REVERT: B 189 TYR cc_start: 0.7510 (m-10) cc_final: 0.7123 (m-80) REVERT: C 82 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6944 (mt) REVERT: D 40 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7461 (mp0) REVERT: D 84 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7145 (mtt180) outliers start: 24 outliers final: 11 residues processed: 138 average time/residue: 1.2646 time to fit residues: 188.6600 Evaluate side-chains 123 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.0980 chunk 110 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.169066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121355 restraints weight = 11986.470| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.21 r_work: 0.3085 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11219 Z= 0.187 Angle : 0.583 11.672 15288 Z= 0.283 Chirality : 0.042 0.280 1828 Planarity : 0.004 0.042 1848 Dihedral : 7.770 59.925 2104 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 1.67 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.24), residues: 1322 helix: 1.98 (0.20), residues: 744 sheet: -0.71 (0.47), residues: 127 loop : -1.54 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.005 0.001 HIS C 197 PHE 0.030 0.001 PHE A 302 TYR 0.014 0.001 TYR A 337 ARG 0.007 0.000 ARG D 84 ********************** 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 131 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7572 (pt0) cc_final: 0.7138 (mm-30) REVERT: A 46 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7712 (mptp) REVERT: A 77 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7334 (mm-30) REVERT: A 81 ASP cc_start: 0.7831 (m-30) cc_final: 0.7580 (m-30) REVERT: A 114 ARG cc_start: 0.6531 (mtt-85) cc_final: 0.6206 (mtp85) REVERT: A 139 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7925 (tp40) REVERT: A 283 ASP cc_start: 0.8050 (p0) cc_final: 0.7775 (p0) REVERT: A 317 ASP cc_start: 0.7430 (p0) cc_final: 0.7139 (p0) REVERT: A 351 LYS cc_start: 0.7545 (mmtp) cc_final: 0.7123 (mtpp) REVERT: A 364 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7861 (tp30) REVERT: A 384 SER cc_start: 0.7432 (OUTLIER) cc_final: 0.6752 (m) REVERT: A 420 GLN cc_start: 0.8054 (pt0) cc_final: 0.7646 (pt0) REVERT: A 474 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 500 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6120 (tt0) REVERT: A 543 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.6924 (mtm180) REVERT: A 619 ARG cc_start: 0.6776 (pmm-80) cc_final: 0.6521 (ptt90) REVERT: A 693 LYS cc_start: 0.7878 (mmtp) cc_final: 0.6949 (mtpp) REVERT: B 160 LYS cc_start: 0.7636 (mttm) cc_final: 0.6737 (mppt) REVERT: B 189 TYR cc_start: 0.7579 (m-10) cc_final: 0.7165 (m-80) REVERT: C 82 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6906 (mt) REVERT: D 40 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7531 (mp0) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 1.3152 time to fit residues: 182.1533 Evaluate side-chains 121 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 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 B residue 170 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 192 LEU 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 105 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.170682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124648 restraints weight = 11850.094| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.19 r_work: 0.3246 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11219 Z= 0.168 Angle : 0.572 11.426 15288 Z= 0.277 Chirality : 0.042 0.277 1828 Planarity : 0.004 0.042 1848 Dihedral : 7.463 58.792 2104 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 1.76 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1322 helix: 2.03 (0.20), residues: 743 sheet: -0.74 (0.46), residues: 127 loop : -1.53 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.004 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.013 0.001 TYR A 337 ARG 0.007 0.000 ARG D 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6331.02 seconds wall clock time: 113 minutes 2.13 seconds (6782.13 seconds total)