Starting phenix.real_space_refine on Tue May 13 23:48:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8im7_35572/05_2025/8im7_35572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8im7_35572/05_2025/8im7_35572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8im7_35572/05_2025/8im7_35572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8im7_35572/05_2025/8im7_35572.map" model { file = "/net/cci-nas-00/data/ceres_data/8im7_35572/05_2025/8im7_35572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8im7_35572/05_2025/8im7_35572.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 6941 2.51 5 N 1669 2.21 5 O 1937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10587 Number of models: 1 Model: "" Number of chains: 13 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: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2247 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 2 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: 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: "F" 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: "G" 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 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: 6.57, per 1000 atoms: 0.62 Number of scatterers: 10587 At special positions: 0 Unit cell: (109.79, 95.5173, 131.748, 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 38 16.00 P 2 15.00 O 1937 8.00 N 1669 7.00 C 6941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 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 F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 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 E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 57.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.180A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.006A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.921A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.515A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.257A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.599A pdb=" N GLN A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.748A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.538A pdb=" N SER A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) 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 481 through 502 removed outlier: 3.983A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.870A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.721A pdb=" N ILE A 537 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.810A pdb=" N LEU A 546 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.572A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.724A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.697A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.588A pdb=" N LEU A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 104 Proline residue: B 88 - end of helix removed outlier: 4.047A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 155 removed outlier: 3.537A pdb=" N MET B 139 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 4.581A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.334A 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 219 through 240 removed outlier: 3.599A pdb=" N TYR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.616A pdb=" N ALA B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.569A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.873A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 3.872A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.239A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.948A pdb=" N PHE C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 61 removed outlier: 4.233A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 96 removed outlier: 3.801A pdb=" N GLN C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 3.513A pdb=" N ALA C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 113 through 135 removed outlier: 3.606A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 184 removed outlier: 3.692A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 203 removed outlier: 3.601A 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: 3.750A 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 20 removed outlier: 3.900A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.541A pdb=" N GLY D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 81 removed outlier: 3.770A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.575A pdb=" N TYR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.822A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 212 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.552A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.612A 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: 3.504A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.222A 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: 3.540A pdb=" N VAL B 193 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 515 hydrogen bonds defined for protein. 1485 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: 2.98 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1749 1.32 - 1.45: 3002 1.45 - 1.57: 6043 1.57 - 1.69: 6 1.69 - 1.82: 58 Bond restraints: 10858 Sorted by residual: bond pdb=" N LEU B 435 " pdb=" CA LEU B 435 " ideal model delta sigma weight residual 1.462 1.491 -0.029 7.70e-03 1.69e+04 1.44e+01 bond pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.15e-02 7.56e+03 1.31e+01 bond pdb=" N VAL B 379 " pdb=" CA VAL B 379 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" C5 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.417 1.479 -0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.94e+00 ... (remaining 10853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 14170 2.40 - 4.80: 569 4.80 - 7.19: 51 7.19 - 9.59: 14 9.59 - 11.99: 2 Bond angle restraints: 14806 Sorted by residual: angle pdb=" N LYS B 80 " pdb=" CA LYS B 80 " pdb=" C LYS B 80 " ideal model delta sigma weight residual 113.97 108.11 5.86 1.28e+00 6.10e-01 2.10e+01 angle pdb=" N ASN C 207 " pdb=" CA ASN C 207 " pdb=" C ASN C 207 " ideal model delta sigma weight residual 109.81 119.23 -9.42 2.21e+00 2.05e-01 1.82e+01 angle pdb=" C VAL A 408 " pdb=" CA VAL A 408 " pdb=" CB VAL A 408 " ideal model delta sigma weight residual 110.13 113.76 -3.63 9.70e-01 1.06e+00 1.40e+01 angle pdb=" C ASN A 264 " pdb=" N THR A 265 " pdb=" CA THR A 265 " ideal model delta sigma weight residual 121.54 128.66 -7.12 1.91e+00 2.74e-01 1.39e+01 angle pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N PRO A 93 " ideal model delta sigma weight residual 117.93 121.90 -3.97 1.20e+00 6.94e-01 1.09e+01 ... (remaining 14801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 6404 22.35 - 44.71: 218 44.71 - 67.06: 51 67.06 - 89.41: 26 89.41 - 111.76: 18 Dihedral angle restraints: 6717 sinusoidal: 2954 harmonic: 3763 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -170.69 84.69 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CA SER A 559 " pdb=" C SER A 559 " pdb=" N PRO A 560 " pdb=" CA PRO A 560 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 6714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1611 0.104 - 0.207: 147 0.207 - 0.311: 9 0.311 - 0.414: 4 0.414 - 0.518: 1 Chirality restraints: 1772 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C17 CLR C 302 " pdb=" C13 CLR C 302 " pdb=" C16 CLR C 302 " pdb=" C20 CLR C 302 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1769 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.044 5.00e-02 4.00e+02 6.53e-02 6.81e+00 pdb=" N PRO A 560 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 565 " -0.019 2.00e-02 2.50e+03 1.76e-02 6.19e+00 pdb=" CG TYR A 565 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 565 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 565 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 565 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 565 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 565 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 565 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.015 2.00e-02 2.50e+03 1.52e-02 5.76e+00 pdb=" CG TRP C 227 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.002 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2338 2.78 - 3.31: 9478 3.31 - 3.84: 17189 3.84 - 4.37: 19498 4.37 - 4.90: 34384 Nonbonded interactions: 82887 Sorted by model distance: nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.245 3.040 nonbonded pdb=" O SER A 234 " pdb=" OG SER A 238 " model vdw 2.295 3.040 nonbonded pdb=" O PHE B 86 " pdb=" OG1 THR B 90 " model vdw 2.299 3.040 nonbonded pdb=" CD2 LEU B 381 " pdb=" CE2 PHE B 386 " model vdw 2.311 3.760 nonbonded pdb=" O LEU B 174 " pdb=" OG SER B 178 " model vdw 2.316 3.040 ... (remaining 82882 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.410 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.650 Find NCS groups from input model: 0.150 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 0.081 10883 Z= 0.437 Angle : 1.096 14.087 14877 Z= 0.572 Chirality : 0.064 0.518 1772 Planarity : 0.007 0.065 1790 Dihedral : 14.519 111.763 4279 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.90 % Allowed : 1.90 % Favored : 97.20 % 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: -4.06 (0.18), residues: 1277 helix: -2.21 (0.15), residues: 674 sheet: -2.30 (0.43), residues: 128 loop : -3.36 (0.22), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 227 HIS 0.021 0.003 HIS C 197 PHE 0.039 0.004 PHE C 132 TYR 0.042 0.003 TYR A 565 ARG 0.011 0.001 ARG A 626 Details of bonding type rmsd link_NAG-ASN : bond 0.01210 ( 12) link_NAG-ASN : angle 5.26868 ( 36) link_BETA1-4 : bond 0.00541 ( 7) link_BETA1-4 : angle 2.59228 ( 21) hydrogen bonds : bond 0.17380 ( 515) hydrogen bonds : angle 6.87977 ( 1485) link_BETA1-6 : bond 0.00402 ( 1) link_BETA1-6 : angle 1.48720 ( 3) SS BOND : bond 0.00554 ( 4) SS BOND : angle 2.93850 ( 8) link_BETA1-3 : bond 0.00096 ( 1) link_BETA1-3 : angle 0.64441 ( 3) covalent geometry : bond 0.00967 (10858) covalent geometry : angle 1.06014 (14806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8975 (mmt) cc_final: 0.8712 (mmm) REVERT: A 414 ARG cc_start: 0.8621 (ttt90) cc_final: 0.8404 (ttm-80) REVERT: A 612 ASN cc_start: 0.8241 (m-40) cc_final: 0.7836 (t0) REVERT: A 649 THR cc_start: 0.9522 (p) cc_final: 0.9282 (p) REVERT: A 652 ARG cc_start: 0.8564 (mtp85) cc_final: 0.7968 (mtt180) REVERT: A 689 CYS cc_start: 0.8555 (t) cc_final: 0.8269 (t) REVERT: B 134 LEU cc_start: 0.8197 (mp) cc_final: 0.7963 (tp) REVERT: B 146 MET cc_start: 0.7454 (mmt) cc_final: 0.7218 (mmt) REVERT: B 244 TRP cc_start: 0.6966 (m-10) cc_final: 0.6355 (m100) REVERT: C 116 GLN cc_start: 0.8283 (mt0) cc_final: 0.7999 (mt0) REVERT: C 180 ASP cc_start: 0.8995 (t70) cc_final: 0.8554 (t0) REVERT: C 183 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7957 (mm-30) REVERT: D 34 ILE cc_start: 0.7041 (mt) cc_final: 0.6786 (mt) REVERT: D 52 GLN cc_start: 0.7668 (tt0) cc_final: 0.7213 (mm-40) REVERT: D 93 SER cc_start: 0.9623 (t) cc_final: 0.9317 (p) outliers start: 10 outliers final: 4 residues processed: 214 average time/residue: 0.2472 time to fit residues: 71.6187 Evaluate side-chains 112 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 149 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 313 GLN A 355 GLN A 454 GLN A 531 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS B 112 GLN B 222 GLN B 405 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079518 restraints weight = 21714.240| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.00 r_work: 0.2889 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10883 Z= 0.125 Angle : 0.669 11.303 14877 Z= 0.326 Chirality : 0.044 0.270 1772 Planarity : 0.005 0.056 1790 Dihedral : 12.929 113.078 2029 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.81 % Allowed : 8.23 % Favored : 89.96 % 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: -1.95 (0.22), residues: 1277 helix: -0.20 (0.19), residues: 677 sheet: -1.97 (0.43), residues: 125 loop : -2.68 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.018 0.001 TYR B 446 ARG 0.007 0.001 ARG C 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 12) link_NAG-ASN : angle 3.39617 ( 36) link_BETA1-4 : bond 0.00419 ( 7) link_BETA1-4 : angle 1.48402 ( 21) hydrogen bonds : bond 0.04502 ( 515) hydrogen bonds : angle 4.52697 ( 1485) link_BETA1-6 : bond 0.01740 ( 1) link_BETA1-6 : angle 2.23655 ( 3) SS BOND : bond 0.00455 ( 4) SS BOND : angle 1.12961 ( 8) link_BETA1-3 : bond 0.00837 ( 1) link_BETA1-3 : angle 1.56073 ( 3) covalent geometry : bond 0.00263 (10858) covalent geometry : angle 0.64519 (14806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.9321 (tpp) cc_final: 0.9108 (tpp) REVERT: A 414 ARG cc_start: 0.8887 (ttt90) cc_final: 0.8473 (ttm-80) REVERT: A 612 ASN cc_start: 0.8449 (m-40) cc_final: 0.8007 (t0) REVERT: A 652 ARG cc_start: 0.8785 (mtp85) cc_final: 0.8423 (mtt180) REVERT: A 683 SER cc_start: 0.9087 (t) cc_final: 0.8822 (p) REVERT: A 689 CYS cc_start: 0.8870 (t) cc_final: 0.8654 (t) REVERT: B 134 LEU cc_start: 0.8206 (mp) cc_final: 0.7950 (tp) REVERT: B 184 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 216 LYS cc_start: 0.7944 (tppt) cc_final: 0.7576 (tttt) REVERT: B 244 TRP cc_start: 0.6846 (m-10) cc_final: 0.6204 (m100) REVERT: B 458 ASP cc_start: 0.8703 (m-30) cc_final: 0.8453 (m-30) REVERT: C 116 GLN cc_start: 0.8620 (mt0) cc_final: 0.8182 (mt0) REVERT: C 180 ASP cc_start: 0.8844 (t70) cc_final: 0.8387 (t0) REVERT: D 34 ILE cc_start: 0.7198 (mt) cc_final: 0.6931 (mt) REVERT: D 36 TRP cc_start: 0.7925 (t60) cc_final: 0.7220 (t60) REVERT: D 40 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6947 (mp0) REVERT: D 52 GLN cc_start: 0.7622 (tt0) cc_final: 0.7119 (mm-40) outliers start: 20 outliers final: 11 residues processed: 154 average time/residue: 0.2214 time to fit residues: 48.9273 Evaluate side-chains 118 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 606 GLN B 222 GLN C 136 ASN D 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.072857 restraints weight = 22868.241| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.97 r_work: 0.2767 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 10883 Z= 0.340 Angle : 0.810 14.270 14877 Z= 0.389 Chirality : 0.049 0.286 1772 Planarity : 0.005 0.058 1790 Dihedral : 11.297 111.592 2027 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.53 % Allowed : 9.86 % Favored : 86.62 % 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: -1.45 (0.23), residues: 1277 helix: 0.30 (0.20), residues: 686 sheet: -2.02 (0.43), residues: 121 loop : -2.56 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 36 HIS 0.009 0.002 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.022 0.002 TYR B 189 ARG 0.003 0.001 ARG A 371 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 12) link_NAG-ASN : angle 3.54225 ( 36) link_BETA1-4 : bond 0.00290 ( 7) link_BETA1-4 : angle 1.78981 ( 21) hydrogen bonds : bond 0.05141 ( 515) hydrogen bonds : angle 4.48687 ( 1485) link_BETA1-6 : bond 0.01790 ( 1) link_BETA1-6 : angle 1.99563 ( 3) SS BOND : bond 0.00643 ( 4) SS BOND : angle 1.44784 ( 8) link_BETA1-3 : bond 0.00813 ( 1) link_BETA1-3 : angle 1.37410 ( 3) covalent geometry : bond 0.00802 (10858) covalent geometry : angle 0.78833 (14806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 612 ASN cc_start: 0.8467 (m-40) cc_final: 0.7970 (t0) REVERT: A 652 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8375 (mtt180) REVERT: B 134 LEU cc_start: 0.8095 (mp) cc_final: 0.7779 (tt) REVERT: B 184 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8561 (mm-30) REVERT: B 244 TRP cc_start: 0.7121 (m-10) cc_final: 0.6404 (m100) REVERT: B 454 GLN cc_start: 0.8827 (tp40) cc_final: 0.8586 (tp40) REVERT: C 109 ARG cc_start: 0.7631 (ptp-110) cc_final: 0.7305 (ptm160) REVERT: C 116 GLN cc_start: 0.8822 (mt0) cc_final: 0.8236 (mt0) REVERT: D 34 ILE cc_start: 0.7355 (mt) cc_final: 0.7100 (mt) REVERT: D 40 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7123 (mp0) REVERT: D 52 GLN cc_start: 0.7689 (tt0) cc_final: 0.7236 (mm-40) outliers start: 39 outliers final: 26 residues processed: 124 average time/residue: 0.1904 time to fit residues: 35.5174 Evaluate side-chains 115 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 385 GLN B 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077260 restraints weight = 21785.139| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.95 r_work: 0.2836 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10883 Z= 0.125 Angle : 0.615 12.438 14877 Z= 0.293 Chirality : 0.043 0.258 1772 Planarity : 0.004 0.053 1790 Dihedral : 10.151 106.137 2027 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.26 % Allowed : 11.57 % Favored : 86.17 % 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: -0.78 (0.24), residues: 1277 helix: 0.88 (0.20), residues: 685 sheet: -1.96 (0.44), residues: 126 loop : -2.25 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 165 HIS 0.004 0.001 HIS C 197 PHE 0.027 0.001 PHE A 302 TYR 0.017 0.001 TYR B 446 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 12) link_NAG-ASN : angle 2.81588 ( 36) link_BETA1-4 : bond 0.00367 ( 7) link_BETA1-4 : angle 1.32345 ( 21) hydrogen bonds : bond 0.03962 ( 515) hydrogen bonds : angle 4.12852 ( 1485) link_BETA1-6 : bond 0.01459 ( 1) link_BETA1-6 : angle 2.34663 ( 3) SS BOND : bond 0.00531 ( 4) SS BOND : angle 0.90650 ( 8) link_BETA1-3 : bond 0.00821 ( 1) link_BETA1-3 : angle 1.42636 ( 3) covalent geometry : bond 0.00276 (10858) covalent geometry : angle 0.59723 (14806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8315 (mt) REVERT: A 612 ASN cc_start: 0.8438 (m-40) cc_final: 0.7922 (t0) REVERT: A 652 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8334 (mtt180) REVERT: B 134 LEU cc_start: 0.8224 (mp) cc_final: 0.7840 (tt) REVERT: B 184 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8480 (mm-30) REVERT: B 244 TRP cc_start: 0.7095 (m-10) cc_final: 0.6368 (m100) REVERT: B 454 GLN cc_start: 0.8752 (tp40) cc_final: 0.8389 (tp-100) REVERT: B 458 ASP cc_start: 0.8570 (m-30) cc_final: 0.8356 (m-30) REVERT: C 101 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7900 (tt) REVERT: C 116 GLN cc_start: 0.8667 (mt0) cc_final: 0.8123 (mt0) REVERT: D 34 ILE cc_start: 0.7250 (mt) cc_final: 0.7004 (mt) REVERT: D 40 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7003 (mp0) REVERT: D 52 GLN cc_start: 0.7557 (tt0) cc_final: 0.7175 (mm-40) outliers start: 25 outliers final: 16 residues processed: 120 average time/residue: 0.1896 time to fit residues: 34.7506 Evaluate side-chains 114 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 243 LEU 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: 127 random chunks: chunk 39 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.076790 restraints weight = 21984.622| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.94 r_work: 0.2822 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10883 Z= 0.168 Angle : 0.624 13.118 14877 Z= 0.297 Chirality : 0.044 0.263 1772 Planarity : 0.004 0.053 1790 Dihedral : 9.649 99.153 2027 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.35 % Allowed : 11.57 % Favored : 85.08 % 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: -0.48 (0.24), residues: 1277 helix: 1.14 (0.20), residues: 687 sheet: -1.83 (0.44), residues: 128 loop : -2.13 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.005 0.001 HIS C 58 PHE 0.028 0.001 PHE A 302 TYR 0.016 0.001 TYR B 446 ARG 0.003 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 12) link_NAG-ASN : angle 2.66917 ( 36) link_BETA1-4 : bond 0.00243 ( 7) link_BETA1-4 : angle 1.42142 ( 21) hydrogen bonds : bond 0.03967 ( 515) hydrogen bonds : angle 4.06090 ( 1485) link_BETA1-6 : bond 0.01510 ( 1) link_BETA1-6 : angle 2.73617 ( 3) SS BOND : bond 0.00412 ( 4) SS BOND : angle 1.39726 ( 8) link_BETA1-3 : bond 0.00827 ( 1) link_BETA1-3 : angle 1.86717 ( 3) covalent geometry : bond 0.00394 (10858) covalent geometry : angle 0.60664 (14806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8123 (t0) cc_final: 0.7760 (t0) REVERT: A 612 ASN cc_start: 0.8447 (m-40) cc_final: 0.7935 (t0) REVERT: A 652 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8330 (mtt180) REVERT: B 134 LEU cc_start: 0.8063 (mp) cc_final: 0.7757 (tt) REVERT: B 184 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8479 (mm-30) REVERT: B 244 TRP cc_start: 0.7146 (m-10) cc_final: 0.6385 (m100) REVERT: B 454 GLN cc_start: 0.8754 (tp40) cc_final: 0.8359 (tp-100) REVERT: C 67 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6723 (tt) REVERT: C 71 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8179 (mp) REVERT: C 101 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7957 (tt) REVERT: C 116 GLN cc_start: 0.8758 (mt0) cc_final: 0.8154 (mt0) REVERT: C 192 LEU cc_start: 0.8909 (tp) cc_final: 0.8507 (tt) REVERT: D 34 ILE cc_start: 0.7379 (mt) cc_final: 0.7119 (mt) REVERT: D 40 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6978 (mp0) REVERT: D 52 GLN cc_start: 0.7595 (tt0) cc_final: 0.7220 (mm-40) outliers start: 37 outliers final: 24 residues processed: 127 average time/residue: 0.1681 time to fit residues: 33.4624 Evaluate side-chains 121 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL 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 605 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 16 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 7.9990 chunk 100 optimal weight: 0.0040 chunk 88 optimal weight: 3.9990 overall best weight: 2.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.076743 restraints weight = 21977.703| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.92 r_work: 0.2832 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10883 Z= 0.170 Angle : 0.619 13.183 14877 Z= 0.293 Chirality : 0.043 0.256 1772 Planarity : 0.004 0.051 1790 Dihedral : 9.210 89.581 2027 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.35 % Allowed : 11.66 % Favored : 84.99 % 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: 1277 helix: 1.31 (0.20), residues: 687 sheet: -1.72 (0.44), residues: 128 loop : -2.06 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.005 0.001 HIS C 58 PHE 0.028 0.001 PHE A 302 TYR 0.015 0.001 TYR B 189 ARG 0.003 0.000 ARG C 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 12) link_NAG-ASN : angle 2.53110 ( 36) link_BETA1-4 : bond 0.00249 ( 7) link_BETA1-4 : angle 1.36365 ( 21) hydrogen bonds : bond 0.03896 ( 515) hydrogen bonds : angle 4.01311 ( 1485) link_BETA1-6 : bond 0.01550 ( 1) link_BETA1-6 : angle 3.24135 ( 3) SS BOND : bond 0.00397 ( 4) SS BOND : angle 1.17251 ( 8) link_BETA1-3 : bond 0.00830 ( 1) link_BETA1-3 : angle 2.17365 ( 3) covalent geometry : bond 0.00400 (10858) covalent geometry : angle 0.60204 (14806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8136 (t0) cc_final: 0.7885 (t0) REVERT: A 612 ASN cc_start: 0.8480 (m-40) cc_final: 0.7994 (t0) REVERT: A 652 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8331 (mtt180) REVERT: B 134 LEU cc_start: 0.8095 (mp) cc_final: 0.7778 (tt) REVERT: B 184 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8465 (mm-30) REVERT: B 244 TRP cc_start: 0.7201 (m-10) cc_final: 0.6376 (m100) REVERT: B 454 GLN cc_start: 0.8731 (tp40) cc_final: 0.8406 (tp-100) REVERT: C 48 LEU cc_start: 0.8766 (mt) cc_final: 0.8342 (tp) REVERT: C 101 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7991 (tt) REVERT: C 109 ARG cc_start: 0.7379 (ptp-110) cc_final: 0.7127 (ptm-80) REVERT: C 116 GLN cc_start: 0.8717 (mt0) cc_final: 0.8093 (mt0) REVERT: D 34 ILE cc_start: 0.7440 (mt) cc_final: 0.7190 (mt) REVERT: D 40 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6921 (mp0) REVERT: D 52 GLN cc_start: 0.7663 (tt0) cc_final: 0.7294 (mm-40) outliers start: 37 outliers final: 28 residues processed: 134 average time/residue: 0.1755 time to fit residues: 36.4457 Evaluate side-chains 125 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL 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 605 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 0.0970 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.078024 restraints weight = 22043.956| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.95 r_work: 0.2862 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10883 Z= 0.107 Angle : 0.576 11.941 14877 Z= 0.271 Chirality : 0.042 0.241 1772 Planarity : 0.003 0.048 1790 Dihedral : 8.713 78.981 2027 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.98 % Allowed : 12.93 % Favored : 84.09 % 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: -0.02 (0.25), residues: 1277 helix: 1.54 (0.21), residues: 685 sheet: -1.60 (0.45), residues: 128 loop : -1.96 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 257 HIS 0.004 0.001 HIS C 58 PHE 0.028 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 12) link_NAG-ASN : angle 2.22303 ( 36) link_BETA1-4 : bond 0.00330 ( 7) link_BETA1-4 : angle 1.20856 ( 21) hydrogen bonds : bond 0.03426 ( 515) hydrogen bonds : angle 3.91332 ( 1485) link_BETA1-6 : bond 0.01391 ( 1) link_BETA1-6 : angle 3.64035 ( 3) SS BOND : bond 0.00306 ( 4) SS BOND : angle 1.50039 ( 8) link_BETA1-3 : bond 0.00933 ( 1) link_BETA1-3 : angle 1.92759 ( 3) covalent geometry : bond 0.00234 (10858) covalent geometry : angle 0.56072 (14806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 548 ASP cc_start: 0.8084 (t0) cc_final: 0.7708 (t0) REVERT: A 612 ASN cc_start: 0.8459 (m-40) cc_final: 0.7975 (t0) REVERT: A 652 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8279 (mtt180) REVERT: B 134 LEU cc_start: 0.8074 (mp) cc_final: 0.7765 (tt) REVERT: B 184 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8391 (mm-30) REVERT: B 244 TRP cc_start: 0.7101 (m-10) cc_final: 0.6302 (m100) REVERT: B 385 ASP cc_start: 0.8636 (m-30) cc_final: 0.8033 (m-30) REVERT: B 454 GLN cc_start: 0.8626 (tp40) cc_final: 0.8231 (tp-100) REVERT: C 48 LEU cc_start: 0.8703 (mt) cc_final: 0.8301 (tp) REVERT: C 67 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6610 (tt) REVERT: C 71 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 101 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7945 (tt) REVERT: C 109 ARG cc_start: 0.7461 (ptp-110) cc_final: 0.7224 (ptm-80) REVERT: C 116 GLN cc_start: 0.8664 (mt0) cc_final: 0.8001 (mt0) REVERT: D 34 ILE cc_start: 0.7450 (mt) cc_final: 0.7214 (mt) REVERT: D 40 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6869 (mp0) REVERT: D 52 GLN cc_start: 0.7606 (tt0) cc_final: 0.7244 (mm-40) outliers start: 33 outliers final: 25 residues processed: 130 average time/residue: 0.1748 time to fit residues: 35.6536 Evaluate side-chains 128 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 63 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 9 optimal weight: 6.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.076703 restraints weight = 22051.370| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.92 r_work: 0.2828 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10883 Z= 0.169 Angle : 0.619 13.522 14877 Z= 0.292 Chirality : 0.043 0.237 1772 Planarity : 0.004 0.049 1790 Dihedral : 8.485 73.757 2027 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.44 % Allowed : 13.11 % Favored : 83.45 % 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: 0.04 (0.25), residues: 1277 helix: 1.54 (0.20), residues: 692 sheet: -1.41 (0.48), residues: 116 loop : -1.97 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 PHE 0.026 0.001 PHE A 302 TYR 0.014 0.001 TYR B 446 ARG 0.002 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 12) link_NAG-ASN : angle 2.39632 ( 36) link_BETA1-4 : bond 0.00211 ( 7) link_BETA1-4 : angle 1.36164 ( 21) hydrogen bonds : bond 0.03771 ( 515) hydrogen bonds : angle 3.95597 ( 1485) link_BETA1-6 : bond 0.01204 ( 1) link_BETA1-6 : angle 3.92549 ( 3) SS BOND : bond 0.00351 ( 4) SS BOND : angle 1.46131 ( 8) link_BETA1-3 : bond 0.00815 ( 1) link_BETA1-3 : angle 2.24135 ( 3) covalent geometry : bond 0.00397 (10858) covalent geometry : angle 0.60228 (14806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8202 (t0) cc_final: 0.7946 (t0) REVERT: A 612 ASN cc_start: 0.8483 (m-40) cc_final: 0.8002 (t0) REVERT: A 652 ARG cc_start: 0.8879 (mtp85) cc_final: 0.8320 (mtt180) REVERT: B 134 LEU cc_start: 0.8101 (mp) cc_final: 0.7808 (tt) REVERT: B 184 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 222 GLN cc_start: 0.8559 (tt0) cc_final: 0.8174 (pt0) REVERT: B 244 TRP cc_start: 0.7099 (m-10) cc_final: 0.6243 (m100) REVERT: B 454 GLN cc_start: 0.8687 (tp40) cc_final: 0.8327 (tp-100) REVERT: C 48 LEU cc_start: 0.8743 (mt) cc_final: 0.8284 (tp) REVERT: C 67 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6662 (tt) REVERT: C 71 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8008 (mp) REVERT: C 101 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8005 (tt) REVERT: C 116 GLN cc_start: 0.8713 (mt0) cc_final: 0.8079 (mt0) REVERT: D 34 ILE cc_start: 0.7415 (mt) cc_final: 0.7165 (mt) REVERT: D 40 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6868 (mp0) REVERT: D 52 GLN cc_start: 0.7658 (tt0) cc_final: 0.7303 (mm-40) outliers start: 38 outliers final: 30 residues processed: 130 average time/residue: 0.1805 time to fit residues: 36.2074 Evaluate side-chains 132 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 12 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.0060 chunk 108 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.074207 restraints weight = 22614.435| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.03 r_work: 0.2794 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10883 Z= 0.223 Angle : 0.668 15.256 14877 Z= 0.318 Chirality : 0.045 0.229 1772 Planarity : 0.004 0.049 1790 Dihedral : 8.333 73.861 2027 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.16 % Allowed : 13.65 % Favored : 83.18 % 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: 0.01 (0.25), residues: 1277 helix: 1.49 (0.20), residues: 689 sheet: -1.33 (0.47), residues: 118 loop : -1.94 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.005 0.001 HIS C 58 PHE 0.026 0.002 PHE A 302 TYR 0.017 0.002 TYR B 189 ARG 0.004 0.000 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 2.52971 ( 36) link_BETA1-4 : bond 0.00233 ( 7) link_BETA1-4 : angle 1.48356 ( 21) hydrogen bonds : bond 0.04174 ( 515) hydrogen bonds : angle 4.05480 ( 1485) link_BETA1-6 : bond 0.00869 ( 1) link_BETA1-6 : angle 4.27704 ( 3) SS BOND : bond 0.00423 ( 4) SS BOND : angle 1.45261 ( 8) link_BETA1-3 : bond 0.00751 ( 1) link_BETA1-3 : angle 2.50961 ( 3) covalent geometry : bond 0.00527 (10858) covalent geometry : angle 0.65125 (14806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8298 (t0) cc_final: 0.8074 (t0) REVERT: A 612 ASN cc_start: 0.8449 (m-40) cc_final: 0.7994 (t0) REVERT: A 652 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8329 (mtt180) REVERT: B 134 LEU cc_start: 0.8109 (mp) cc_final: 0.7808 (tt) REVERT: B 184 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 222 GLN cc_start: 0.8498 (tt0) cc_final: 0.8173 (pt0) REVERT: B 244 TRP cc_start: 0.7040 (m-10) cc_final: 0.6202 (m100) REVERT: B 247 TRP cc_start: 0.7693 (m100) cc_final: 0.7390 (m100) REVERT: B 454 GLN cc_start: 0.8705 (tp40) cc_final: 0.8339 (tp-100) REVERT: C 71 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8041 (mp) REVERT: C 101 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8052 (tt) REVERT: C 116 GLN cc_start: 0.8746 (mt0) cc_final: 0.8129 (mt0) REVERT: D 34 ILE cc_start: 0.7412 (mt) cc_final: 0.7162 (mt) REVERT: D 40 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6879 (mp0) REVERT: D 52 GLN cc_start: 0.7657 (tt0) cc_final: 0.7289 (mm-40) outliers start: 35 outliers final: 31 residues processed: 125 average time/residue: 0.1699 time to fit residues: 33.2166 Evaluate side-chains 128 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 0.0020 chunk 57 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.078026 restraints weight = 21973.944| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.90 r_work: 0.2869 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10883 Z= 0.101 Angle : 0.575 12.150 14877 Z= 0.273 Chirality : 0.042 0.241 1772 Planarity : 0.004 0.048 1790 Dihedral : 7.756 73.775 2027 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.35 % Allowed : 14.38 % Favored : 83.27 % 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: 0.30 (0.25), residues: 1277 helix: 1.69 (0.20), residues: 692 sheet: -1.23 (0.46), residues: 129 loop : -1.76 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 257 HIS 0.004 0.001 HIS C 58 PHE 0.028 0.001 PHE A 302 TYR 0.013 0.001 TYR A 569 ARG 0.002 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 12) link_NAG-ASN : angle 2.12017 ( 36) link_BETA1-4 : bond 0.00411 ( 7) link_BETA1-4 : angle 1.17746 ( 21) hydrogen bonds : bond 0.03372 ( 515) hydrogen bonds : angle 3.88658 ( 1485) link_BETA1-6 : bond 0.00407 ( 1) link_BETA1-6 : angle 4.04921 ( 3) SS BOND : bond 0.00233 ( 4) SS BOND : angle 1.00419 ( 8) link_BETA1-3 : bond 0.00980 ( 1) link_BETA1-3 : angle 1.89581 ( 3) covalent geometry : bond 0.00216 (10858) covalent geometry : angle 0.56071 (14806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8172 (t0) cc_final: 0.7925 (t0) REVERT: A 612 ASN cc_start: 0.8446 (m-40) cc_final: 0.8015 (t0) REVERT: A 652 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8527 (mtt180) REVERT: B 134 LEU cc_start: 0.8212 (mp) cc_final: 0.7902 (tt) REVERT: B 184 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 222 GLN cc_start: 0.8477 (tt0) cc_final: 0.8214 (pt0) REVERT: B 244 TRP cc_start: 0.7083 (m-10) cc_final: 0.6249 (m100) REVERT: C 48 LEU cc_start: 0.8686 (mt) cc_final: 0.8257 (tp) REVERT: C 67 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6662 (tt) REVERT: C 71 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 101 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7914 (tt) REVERT: C 116 GLN cc_start: 0.8658 (mt0) cc_final: 0.8112 (mt0) REVERT: D 34 ILE cc_start: 0.7496 (mt) cc_final: 0.7243 (mt) REVERT: D 40 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6963 (mp0) REVERT: D 52 GLN cc_start: 0.7591 (tt0) cc_final: 0.7258 (mm-40) outliers start: 26 outliers final: 20 residues processed: 124 average time/residue: 0.1708 time to fit residues: 33.3289 Evaluate side-chains 120 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074774 restraints weight = 22476.529| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.95 r_work: 0.2808 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10883 Z= 0.199 Angle : 0.635 14.375 14877 Z= 0.304 Chirality : 0.044 0.235 1772 Planarity : 0.004 0.050 1790 Dihedral : 7.688 73.416 2025 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.62 % Allowed : 14.10 % Favored : 83.27 % 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 (0.25), residues: 1277 helix: 1.65 (0.20), residues: 690 sheet: -0.99 (0.49), residues: 115 loop : -1.84 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.005 0.001 HIS C 58 PHE 0.026 0.001 PHE A 302 TYR 0.015 0.001 TYR B 446 ARG 0.003 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 12) link_NAG-ASN : angle 2.36962 ( 36) link_BETA1-4 : bond 0.00224 ( 7) link_BETA1-4 : angle 1.43969 ( 21) hydrogen bonds : bond 0.03921 ( 515) hydrogen bonds : angle 3.96471 ( 1485) link_BETA1-6 : bond 0.00344 ( 1) link_BETA1-6 : angle 3.66119 ( 3) SS BOND : bond 0.00344 ( 4) SS BOND : angle 1.25610 ( 8) link_BETA1-3 : bond 0.00751 ( 1) link_BETA1-3 : angle 2.49050 ( 3) covalent geometry : bond 0.00466 (10858) covalent geometry : angle 0.61978 (14806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4137.68 seconds wall clock time: 72 minutes 43.46 seconds (4363.46 seconds total)