Starting phenix.real_space_refine on Thu Jan 23 22:12:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ari_43783/01_2025/9ari_43783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ari_43783/01_2025/9ari_43783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ari_43783/01_2025/9ari_43783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ari_43783/01_2025/9ari_43783.map" model { file = "/net/cci-nas-00/data/ceres_data/9ari_43783/01_2025/9ari_43783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ari_43783/01_2025/9ari_43783.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13348 2.51 5 N 3454 2.21 5 O 3866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 20756 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 5296 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 36, 'TRANS': 764} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1295 Unresolved non-hydrogen dihedrals: 890 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 24, 'TYR:plan': 9, 'ASN:plan1': 24, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 5, 'GLU:plan': 41, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 745 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5072 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 1194 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 36, 'TYR:plan': 17, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 16, 'GLU:plan': 46, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 809 Chain: "C" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 5296 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 36, 'TRANS': 764} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1295 Unresolved non-hydrogen dihedrals: 890 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 24, 'TYR:plan': 9, 'ASN:plan1': 24, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 5, 'GLU:plan': 41, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 745 Chain: "D" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5072 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 1194 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 36, 'TYR:plan': 17, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 16, 'GLU:plan': 46, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 809 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 12.15, per 1000 atoms: 0.59 Number of scatterers: 20756 At special positions: 0 Unit cell: (146.59, 129.47, 180.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3866 8.00 N 3454 7.00 C 13348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.75 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=1.96 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.02 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=1.67 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.75 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 3.1 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 34 sheets defined 42.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.269A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.793A pdb=" N TYR A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 4.071A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.720A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 272 through 275 removed outlier: 3.567A pdb=" N ILE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.906A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.640A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 3.711A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.715A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 removed outlier: 3.572A pdb=" N ARG A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.798A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.571A pdb=" N THR A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 Processing helix chain 'A' and resid 754 through 762 Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.038A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.145A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 862 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.290A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.546A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.107A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.312A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 580 removed outlier: 3.621A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.826A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 709 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 772 through 786 Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.675A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 844 removed outlier: 3.513A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.738A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.268A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.793A pdb=" N TYR C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 4.071A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.720A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 272 through 275 removed outlier: 3.566A pdb=" N ILE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 317 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.906A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.640A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 605 removed outlier: 3.710A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 634 Processing helix chain 'C' and resid 647 through 676 removed outlier: 3.715A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.572A pdb=" N ARG C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.799A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 729 removed outlier: 3.571A pdb=" N THR C 722 " --> pdb=" O VAL C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 744 Processing helix chain 'C' and resid 754 through 762 Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.037A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.145A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 862 " --> pdb=" O TYR C 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 4.290A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.545A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 4.108A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 4.312A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 580 removed outlier: 3.621A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.825A pdb=" N GLN D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 709 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 772 through 786 Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.675A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 794 " --> pdb=" O GLU D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 844 removed outlier: 3.513A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.423A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 138 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.634A pdb=" N LEU A 242 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.925A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 394 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 389 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.778A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.755A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 783 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 549 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 703 removed outlier: 7.022A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 750 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 562 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 560 " --> pdb=" O TRP A 752 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 69 removed outlier: 7.328A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 69 removed outlier: 7.461A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 205 removed outlier: 8.346A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU B 205 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 173 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.854A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 376 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.736A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 455 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 438 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.603A pdb=" N ALA B 509 " --> pdb=" O ALA B 765 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 732 removed outlier: 3.624A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 26 through 33 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.423A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 138 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.633A pdb=" N LEU C 242 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 290 through 292 removed outlier: 6.925A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 394 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 389 " --> pdb=" O HIS C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 360 through 361 removed outlier: 3.779A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 421 through 422 removed outlier: 3.755A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 549 " --> pdb=" O MET C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 703 removed outlier: 7.022A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE C 750 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 562 " --> pdb=" O PHE C 750 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 560 " --> pdb=" O TRP C 752 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.328A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.461A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 205 removed outlier: 8.346A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU D 205 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR D 173 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 278 through 281 removed outlier: 6.855A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 376 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD4, first strand: chain 'D' and resid 405 through 408 Processing sheet with id=AD5, first strand: chain 'D' and resid 434 through 438 removed outlier: 3.736A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 455 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 438 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 453 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 508 through 509 removed outlier: 3.603A pdb=" N ALA D 509 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 730 through 732 removed outlier: 3.624A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3048 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: 7.01 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3398 1.25 - 1.39: 4826 1.39 - 1.54: 12337 1.54 - 1.68: 459 1.68 - 1.82: 136 Bond restraints: 21156 Sorted by residual: bond pdb=" C THR C 669 " pdb=" O THR C 669 " ideal model delta sigma weight residual 1.236 1.110 0.126 1.26e-02 6.30e+03 1.00e+02 bond pdb=" C THR A 669 " pdb=" O THR A 669 " ideal model delta sigma weight residual 1.236 1.111 0.126 1.26e-02 6.30e+03 9.96e+01 bond pdb=" C ASN A 671 " pdb=" O ASN A 671 " ideal model delta sigma weight residual 1.236 1.124 0.113 1.15e-02 7.56e+03 9.62e+01 bond pdb=" C ASN C 671 " pdb=" O ASN C 671 " ideal model delta sigma weight residual 1.236 1.124 0.113 1.15e-02 7.56e+03 9.60e+01 bond pdb=" C ALA C 670 " pdb=" O ALA C 670 " ideal model delta sigma weight residual 1.236 1.132 0.105 1.15e-02 7.56e+03 8.27e+01 ... (remaining 21151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 28848 4.72 - 9.44: 301 9.44 - 14.16: 38 14.16 - 18.89: 7 18.89 - 23.61: 2 Bond angle restraints: 29196 Sorted by residual: angle pdb=" C PHE A 479 " pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " ideal model delta sigma weight residual 110.88 87.27 23.61 1.57e+00 4.06e-01 2.26e+02 angle pdb=" C PHE C 479 " pdb=" CA PHE C 479 " pdb=" CB PHE C 479 " ideal model delta sigma weight residual 110.88 87.29 23.59 1.57e+00 4.06e-01 2.26e+02 angle pdb=" C LEU C 635 " pdb=" N LEU C 636 " pdb=" CA LEU C 636 " ideal model delta sigma weight residual 122.95 106.94 16.01 1.66e+00 3.63e-01 9.30e+01 angle pdb=" N ILE C 797 " pdb=" CA ILE C 797 " pdb=" CB ILE C 797 " ideal model delta sigma weight residual 110.54 123.10 -12.56 1.36e+00 5.41e-01 8.53e+01 angle pdb=" N ILE A 797 " pdb=" CA ILE A 797 " pdb=" CB ILE A 797 " ideal model delta sigma weight residual 110.54 123.09 -12.55 1.36e+00 5.41e-01 8.52e+01 ... (remaining 29191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 11482 14.34 - 28.68: 531 28.68 - 43.02: 205 43.02 - 57.35: 52 57.35 - 71.69: 8 Dihedral angle restraints: 12278 sinusoidal: 3120 harmonic: 9158 Sorted by residual: dihedral pdb=" C PHE A 479 " pdb=" N PHE A 479 " pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " ideal model delta harmonic sigma weight residual -122.60 -93.55 -29.05 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C PHE C 479 " pdb=" N PHE C 479 " pdb=" CA PHE C 479 " pdb=" CB PHE C 479 " ideal model delta harmonic sigma weight residual -122.60 -93.59 -29.01 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C ASN B 615 " pdb=" N ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta harmonic sigma weight residual -122.60 -150.52 27.92 0 2.50e+00 1.60e-01 1.25e+02 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 3707 0.225 - 0.450: 59 0.450 - 0.675: 10 0.675 - 0.900: 4 0.900 - 1.125: 2 Chirality restraints: 3782 Sorted by residual: chirality pdb=" CA ASN B 615 " pdb=" N ASN B 615 " pdb=" C ASN B 615 " pdb=" CB ASN B 615 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.13 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA PHE C 675 " pdb=" N PHE C 675 " pdb=" C PHE C 675 " pdb=" CB PHE C 675 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 3779 not shown) Planarity restraints: 3706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 830 " 0.029 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C THR C 830 " -0.105 2.00e-02 2.50e+03 pdb=" O THR C 830 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS C 831 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 830 " 0.029 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C THR A 830 " -0.104 2.00e-02 2.50e+03 pdb=" O THR A 830 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS A 831 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 616 " -0.027 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ASN B 616 " 0.100 2.00e-02 2.50e+03 pdb=" O ASN B 616 " -0.039 2.00e-02 2.50e+03 pdb=" N SER B 617 " -0.034 2.00e-02 2.50e+03 ... (remaining 3703 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 67 2.43 - 3.05: 14056 3.05 - 3.67: 30282 3.67 - 4.28: 39833 4.28 - 4.90: 65322 Nonbonded interactions: 149560 Sorted by model distance: nonbonded pdb=" O LEU D 513 " pdb=" CG2 THR D 514 " model vdw 1.816 3.460 nonbonded pdb=" O LEU B 513 " pdb=" CG2 THR B 514 " model vdw 1.816 3.460 nonbonded pdb=" O GLY A 459 " pdb=" N ASN A 461 " model vdw 1.891 3.120 nonbonded pdb=" O GLY C 459 " pdb=" N ASN C 461 " model vdw 1.891 3.120 nonbonded pdb=" OG SER A 638 " pdb=" N GLY A 639 " model vdw 1.961 3.120 ... (remaining 149555 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 46.470 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.007 0.126 21156 Z= 0.464 Angle : 1.123 23.607 29196 Z= 0.741 Chirality : 0.075 1.125 3782 Planarity : 0.007 0.063 3706 Dihedral : 10.705 71.692 6288 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.86 % Favored : 92.88 % Rotamer: Outliers : 9.33 % Allowed : 8.80 % Favored : 81.87 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.13), residues: 3148 helix: -0.70 (0.13), residues: 1350 sheet: -3.15 (0.21), residues: 414 loop : -3.47 (0.14), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 632 HIS 0.006 0.001 HIS A 801 PHE 0.039 0.002 PHE A 429 TYR 0.022 0.001 TYR D 843 ARG 0.007 0.001 ARG C 651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 430 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7952 (pp30) REVERT: A 597 MET cc_start: 0.8061 (ttt) cc_final: 0.7525 (ttm) REVERT: A 783 MET cc_start: 0.7913 (tpp) cc_final: 0.7591 (tpp) REVERT: A 801 HIS cc_start: 0.9323 (OUTLIER) cc_final: 0.8852 (t-90) REVERT: B 184 ASN cc_start: 0.8790 (m110) cc_final: 0.8587 (m-40) REVERT: B 232 CYS cc_start: 0.6404 (t) cc_final: 0.5849 (t) REVERT: B 467 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8231 (mptt) REVERT: B 480 LEU cc_start: 0.7577 (tp) cc_final: 0.7241 (tt) REVERT: B 782 GLN cc_start: 0.8326 (pp30) cc_final: 0.8054 (tm-30) REVERT: C 546 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7882 (pp30) REVERT: C 801 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.8455 (t-90) REVERT: D 467 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8002 (mmtm) REVERT: D 782 GLN cc_start: 0.8435 (pp30) cc_final: 0.8090 (tm-30) REVERT: D 795 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9247 (tp) outliers start: 159 outliers final: 68 residues processed: 568 average time/residue: 0.2669 time to fit residues: 248.5936 Evaluate side-chains 365 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 20.0000 chunk 239 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 161 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 247 optimal weight: 50.0000 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 498 HIS A 577 GLN A 792 GLN B 357 GLN B 615 ASN B 710 ASN B 775 GLN C 159 ASN C 498 HIS C 577 GLN C 748 HIS C 792 GLN D 357 GLN D 615 ASN D 710 ASN D 775 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.177114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.143451 restraints weight = 43710.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.134319 restraints weight = 59788.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132130 restraints weight = 47634.453| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21156 Z= 0.256 Angle : 0.628 7.713 29196 Z= 0.331 Chirality : 0.044 0.247 3782 Planarity : 0.004 0.054 3706 Dihedral : 7.197 74.887 3365 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 7.45 % Allowed : 15.90 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3148 helix: 0.32 (0.14), residues: 1344 sheet: -2.70 (0.22), residues: 418 loop : -2.95 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.005 0.001 HIS C 592 PHE 0.035 0.002 PHE A 579 TYR 0.018 0.001 TYR C 599 ARG 0.009 0.001 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 311 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8002 (ttm-80) REVERT: A 775 PHE cc_start: 0.8088 (t80) cc_final: 0.7887 (t80) REVERT: A 801 HIS cc_start: 0.9050 (OUTLIER) cc_final: 0.8386 (t-90) REVERT: B 186 ILE cc_start: 0.9137 (pt) cc_final: 0.8840 (tp) REVERT: B 232 CYS cc_start: 0.6327 (t) cc_final: 0.5749 (t) REVERT: B 240 ILE cc_start: 0.8015 (tp) cc_final: 0.7765 (mt) REVERT: B 357 GLN cc_start: 0.7334 (mt0) cc_final: 0.6541 (pp30) REVERT: B 429 CYS cc_start: 0.4758 (OUTLIER) cc_final: 0.4414 (t) REVERT: B 467 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8214 (mptt) REVERT: B 476 TYR cc_start: 0.8014 (p90) cc_final: 0.7587 (p90) REVERT: C 767 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9222 (pp) REVERT: C 801 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.8274 (t-90) REVERT: D 433 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8014 (t) REVERT: D 467 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8227 (mptt) REVERT: D 709 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7316 (t80) REVERT: D 782 GLN cc_start: 0.8469 (pp30) cc_final: 0.8258 (tm-30) REVERT: D 795 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9341 (tp) outliers start: 127 outliers final: 70 residues processed: 415 average time/residue: 0.2577 time to fit residues: 178.3318 Evaluate side-chains 353 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 275 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 283 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 118 optimal weight: 0.0970 chunk 284 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 186 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 overall best weight: 1.1718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN C 748 HIS D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.176960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.144957 restraints weight = 43632.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139814 restraints weight = 53408.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.137161 restraints weight = 46713.285| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21156 Z= 0.205 Angle : 0.585 8.081 29196 Z= 0.301 Chirality : 0.043 0.214 3782 Planarity : 0.004 0.046 3706 Dihedral : 6.253 73.711 3314 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 7.51 % Allowed : 16.96 % Favored : 75.53 % 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: -1.64 (0.15), residues: 3148 helix: 0.82 (0.14), residues: 1336 sheet: -2.38 (0.23), residues: 428 loop : -2.65 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 635 HIS 0.004 0.001 HIS B 486 PHE 0.024 0.001 PHE A 579 TYR 0.011 0.001 TYR D 507 ARG 0.004 0.000 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 288 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7570 (pt) cc_final: 0.7188 (tp) REVERT: A 797 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8064 (tt) REVERT: A 801 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8217 (t-90) REVERT: B 186 ILE cc_start: 0.9029 (pt) cc_final: 0.8655 (tp) REVERT: B 240 ILE cc_start: 0.7843 (tp) cc_final: 0.7592 (mt) REVERT: B 357 GLN cc_start: 0.7333 (mt0) cc_final: 0.6363 (pp30) REVERT: B 467 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8251 (mptt) REVERT: B 476 TYR cc_start: 0.7999 (p90) cc_final: 0.7597 (p90) REVERT: C 91 LEU cc_start: 0.7605 (pt) cc_final: 0.7166 (tp) REVERT: C 748 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8139 (m170) REVERT: C 767 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9167 (pp) REVERT: C 783 MET cc_start: 0.8132 (tpp) cc_final: 0.7910 (tpp) REVERT: C 797 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7747 (pt) REVERT: C 801 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8131 (t-90) REVERT: D 433 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8012 (t) REVERT: D 467 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8288 (mptt) outliers start: 128 outliers final: 78 residues processed: 390 average time/residue: 0.2953 time to fit residues: 193.2482 Evaluate side-chains 358 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 273 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 748 HIS Chi-restraints excluded: chain C residue 758 GLU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 24 optimal weight: 0.0870 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 50.0000 chunk 134 optimal weight: 1.9990 chunk 272 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 303 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 239 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN B 703 HIS C 748 HIS D 184 ASN D 703 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.174885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.140256 restraints weight = 43872.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.130314 restraints weight = 59545.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.129798 restraints weight = 48126.399| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21156 Z= 0.271 Angle : 0.613 8.565 29196 Z= 0.318 Chirality : 0.044 0.211 3782 Planarity : 0.004 0.043 3706 Dihedral : 6.098 68.431 3301 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 8.33 % Allowed : 17.31 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3148 helix: 0.86 (0.14), residues: 1354 sheet: -2.30 (0.23), residues: 428 loop : -2.57 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.028 0.002 HIS C 748 PHE 0.025 0.002 PHE A 579 TYR 0.011 0.001 TYR A 599 ARG 0.003 0.001 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 277 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4694 (OUTLIER) cc_final: 0.4361 (mm) REVERT: A 91 LEU cc_start: 0.8128 (pt) cc_final: 0.7597 (tp) REVERT: A 797 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8052 (tt) REVERT: A 801 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8221 (t-90) REVERT: B 186 ILE cc_start: 0.9141 (pt) cc_final: 0.8869 (tp) REVERT: B 240 ILE cc_start: 0.8113 (tp) cc_final: 0.7845 (mt) REVERT: B 357 GLN cc_start: 0.7311 (mt0) cc_final: 0.6377 (pp30) REVERT: B 405 HIS cc_start: 0.7416 (t70) cc_final: 0.7167 (t70) REVERT: B 433 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7955 (t) REVERT: B 467 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8183 (mptt) REVERT: C 26 ILE cc_start: 0.4493 (OUTLIER) cc_final: 0.4211 (mm) REVERT: C 91 LEU cc_start: 0.8264 (pt) cc_final: 0.7788 (tp) REVERT: C 767 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9164 (pp) REVERT: C 783 MET cc_start: 0.8186 (tpp) cc_final: 0.7845 (tpp) REVERT: C 797 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7522 (pt) REVERT: C 801 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.8181 (t-90) REVERT: D 357 GLN cc_start: 0.7626 (mt0) cc_final: 0.7186 (pp30) REVERT: D 433 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7964 (t) REVERT: D 795 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9291 (tt) outliers start: 142 outliers final: 93 residues processed: 395 average time/residue: 0.2554 time to fit residues: 167.7849 Evaluate side-chains 362 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 259 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 68 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 279 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 184 ASN D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.180730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.151433 restraints weight = 45544.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.146447 restraints weight = 54554.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.144216 restraints weight = 45637.179| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21156 Z= 0.157 Angle : 0.563 9.780 29196 Z= 0.286 Chirality : 0.042 0.155 3782 Planarity : 0.003 0.045 3706 Dihedral : 5.732 64.179 3299 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 7.28 % Allowed : 18.78 % Favored : 73.94 % 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: -1.13 (0.15), residues: 3148 helix: 1.23 (0.14), residues: 1336 sheet: -1.95 (0.24), residues: 408 loop : -2.43 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 373 HIS 0.004 0.001 HIS C 748 PHE 0.015 0.001 PHE A 579 TYR 0.009 0.001 TYR B 239 ARG 0.002 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 286 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4157 (OUTLIER) cc_final: 0.3889 (mm) REVERT: A 91 LEU cc_start: 0.7507 (pt) cc_final: 0.7217 (tp) REVERT: A 534 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8563 (mm) REVERT: A 587 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7595 (p) REVERT: A 767 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9130 (pp) REVERT: A 801 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8590 (t70) REVERT: B 186 ILE cc_start: 0.8972 (pt) cc_final: 0.8689 (tp) REVERT: B 240 ILE cc_start: 0.7820 (tp) cc_final: 0.7585 (mt) REVERT: B 357 GLN cc_start: 0.7215 (mt0) cc_final: 0.6438 (pp30) REVERT: B 467 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8286 (mptt) REVERT: C 26 ILE cc_start: 0.3994 (OUTLIER) cc_final: 0.3779 (mm) REVERT: C 91 LEU cc_start: 0.7493 (pt) cc_final: 0.7217 (tp) REVERT: C 532 ASP cc_start: 0.8503 (t70) cc_final: 0.8192 (t0) REVERT: C 533 MET cc_start: 0.8209 (ptp) cc_final: 0.7905 (ptp) REVERT: C 767 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9106 (pp) REVERT: C 775 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: C 797 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7733 (pt) REVERT: C 801 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.8618 (t70) REVERT: D 357 GLN cc_start: 0.7351 (mt0) cc_final: 0.6849 (pp30) REVERT: D 467 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8197 (mptt) REVERT: D 795 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9259 (tt) outliers start: 124 outliers final: 78 residues processed: 390 average time/residue: 0.2535 time to fit residues: 164.4340 Evaluate side-chains 357 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 268 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 149 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 272 optimal weight: 40.0000 chunk 246 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.177657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.149254 restraints weight = 45115.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.144475 restraints weight = 58480.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.142132 restraints weight = 52755.060| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21156 Z= 0.272 Angle : 0.618 13.454 29196 Z= 0.316 Chirality : 0.044 0.206 3782 Planarity : 0.004 0.044 3706 Dihedral : 5.509 57.922 3289 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 7.69 % Allowed : 19.66 % Favored : 72.65 % 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: -1.12 (0.15), residues: 3148 helix: 1.19 (0.14), residues: 1322 sheet: -1.89 (0.25), residues: 390 loop : -2.35 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 635 HIS 0.004 0.001 HIS C 592 PHE 0.022 0.002 PHE A 579 TYR 0.012 0.001 TYR B 699 ARG 0.004 0.001 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 267 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4008 (OUTLIER) cc_final: 0.3779 (mm) REVERT: A 91 LEU cc_start: 0.7305 (pt) cc_final: 0.7042 (tp) REVERT: A 767 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9164 (pp) REVERT: A 776 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: A 801 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8245 (t-90) REVERT: B 186 ILE cc_start: 0.8879 (pt) cc_final: 0.8596 (tp) REVERT: B 240 ILE cc_start: 0.7834 (tp) cc_final: 0.7590 (mt) REVERT: B 357 GLN cc_start: 0.7284 (mt0) cc_final: 0.6552 (pp30) REVERT: B 429 CYS cc_start: 0.4996 (OUTLIER) cc_final: 0.4777 (t) REVERT: B 467 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8247 (mptt) REVERT: C 767 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9136 (pp) REVERT: C 775 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: C 783 MET cc_start: 0.7906 (tpp) cc_final: 0.7651 (ttm) REVERT: C 797 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7529 (pt) REVERT: D 357 GLN cc_start: 0.7265 (mt0) cc_final: 0.6860 (pp30) REVERT: D 467 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8228 (mptt) REVERT: D 795 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9200 (tt) outliers start: 131 outliers final: 93 residues processed: 378 average time/residue: 0.2591 time to fit residues: 164.0161 Evaluate side-chains 351 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 250 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 282 optimal weight: 0.9990 chunk 312 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 chunk 262 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 chunk 243 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 184 ASN D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.178728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.149134 restraints weight = 44945.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.141022 restraints weight = 61406.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137771 restraints weight = 56951.357| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21156 Z= 0.327 Angle : 0.652 11.930 29196 Z= 0.337 Chirality : 0.045 0.262 3782 Planarity : 0.004 0.044 3706 Dihedral : 5.690 55.847 3287 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.70 % Favored : 91.23 % Rotamer: Outliers : 7.51 % Allowed : 20.36 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3148 helix: 1.08 (0.14), residues: 1322 sheet: -1.67 (0.26), residues: 392 loop : -2.37 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 559 HIS 0.004 0.001 HIS A 425 PHE 0.026 0.002 PHE A 554 TYR 0.013 0.001 TYR A 599 ARG 0.004 0.001 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 258 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7720 (pt) cc_final: 0.7343 (tp) REVERT: A 801 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8324 (t-90) REVERT: B 186 ILE cc_start: 0.9015 (pt) cc_final: 0.8725 (tp) REVERT: B 240 ILE cc_start: 0.8076 (tp) cc_final: 0.7819 (mt) REVERT: B 357 GLN cc_start: 0.7306 (mt0) cc_final: 0.6580 (pp30) REVERT: B 467 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8236 (mptt) REVERT: B 663 VAL cc_start: 0.6006 (OUTLIER) cc_final: 0.5793 (p) REVERT: B 739 MET cc_start: 0.6870 (mtt) cc_final: 0.6595 (mtt) REVERT: C 767 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9135 (pp) REVERT: C 775 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: C 783 MET cc_start: 0.7950 (tpp) cc_final: 0.7386 (ttm) REVERT: C 797 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.7748 (pt) REVERT: D 357 GLN cc_start: 0.7384 (mt0) cc_final: 0.6927 (pp30) REVERT: D 467 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8263 (mptt) REVERT: D 702 MET cc_start: 0.6313 (mmt) cc_final: 0.6035 (mmt) outliers start: 128 outliers final: 99 residues processed: 360 average time/residue: 0.2601 time to fit residues: 157.2565 Evaluate side-chains 348 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 244 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 224 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 266 optimal weight: 0.1980 chunk 198 optimal weight: 0.2980 chunk 275 optimal weight: 0.1980 chunk 16 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.183729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.154051 restraints weight = 45510.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.146508 restraints weight = 58410.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.143322 restraints weight = 49729.669| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21156 Z= 0.158 Angle : 0.586 12.505 29196 Z= 0.293 Chirality : 0.042 0.211 3782 Planarity : 0.004 0.046 3706 Dihedral : 5.252 56.821 3285 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.22 % Allowed : 23.06 % Favored : 71.71 % 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: -0.80 (0.15), residues: 3148 helix: 1.44 (0.15), residues: 1314 sheet: -1.51 (0.27), residues: 374 loop : -2.22 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 796 HIS 0.002 0.000 HIS D 703 PHE 0.020 0.001 PHE D 637 TYR 0.011 0.001 TYR B 239 ARG 0.006 0.001 ARG C 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 272 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7767 (pt) cc_final: 0.7440 (tp) REVERT: A 526 LEU cc_start: 0.8043 (pp) cc_final: 0.7822 (pp) REVERT: A 776 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.6880 (mmm-85) REVERT: B 186 ILE cc_start: 0.9077 (pt) cc_final: 0.8746 (tp) REVERT: B 240 ILE cc_start: 0.7995 (tp) cc_final: 0.7735 (mt) REVERT: B 357 GLN cc_start: 0.7259 (mt0) cc_final: 0.6525 (pp30) REVERT: B 405 HIS cc_start: 0.6721 (t70) cc_final: 0.6458 (t70) REVERT: B 467 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8208 (mptt) REVERT: C 767 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9118 (pp) REVERT: C 775 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: C 783 MET cc_start: 0.7720 (tpp) cc_final: 0.7410 (ttm) REVERT: D 357 GLN cc_start: 0.7131 (mt0) cc_final: 0.6690 (pp30) REVERT: D 467 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8209 (mptt) REVERT: D 702 MET cc_start: 0.6178 (mmt) cc_final: 0.5936 (mmt) REVERT: D 784 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7323 (t80) outliers start: 89 outliers final: 69 residues processed: 345 average time/residue: 0.2538 time to fit residues: 147.1071 Evaluate side-chains 339 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 267 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 183 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.176774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.147586 restraints weight = 45202.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.140545 restraints weight = 62026.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.137747 restraints weight = 59382.640| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 21156 Z= 0.511 Angle : 0.738 10.907 29196 Z= 0.388 Chirality : 0.047 0.238 3782 Planarity : 0.004 0.047 3706 Dihedral : 5.594 56.469 3280 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.21 % Favored : 90.69 % Rotamer: Outliers : 5.63 % Allowed : 23.00 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3148 helix: 1.09 (0.15), residues: 1308 sheet: -1.62 (0.26), residues: 394 loop : -2.32 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 559 HIS 0.010 0.002 HIS A 801 PHE 0.034 0.003 PHE A 554 TYR 0.021 0.002 TYR A 668 ARG 0.004 0.001 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 249 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7456 (pt) cc_final: 0.7243 (tp) REVERT: A 776 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7267 (mmm-85) REVERT: B 186 ILE cc_start: 0.8957 (pt) cc_final: 0.8600 (tp) REVERT: B 240 ILE cc_start: 0.7975 (tp) cc_final: 0.7709 (mt) REVERT: B 357 GLN cc_start: 0.7325 (mt0) cc_final: 0.6668 (pp30) REVERT: B 467 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8220 (mptt) REVERT: C 767 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9158 (pp) REVERT: C 775 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: C 783 MET cc_start: 0.8106 (tpp) cc_final: 0.7596 (ttm) REVERT: D 357 GLN cc_start: 0.7362 (mt0) cc_final: 0.7115 (pp30) outliers start: 96 outliers final: 79 residues processed: 328 average time/residue: 0.2632 time to fit residues: 145.9708 Evaluate side-chains 328 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 247 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 145 optimal weight: 10.0000 chunk 165 optimal weight: 0.1980 chunk 281 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 chunk 273 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.179991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.150267 restraints weight = 45117.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.140906 restraints weight = 56669.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.137893 restraints weight = 55749.662| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21156 Z= 0.248 Angle : 0.625 11.730 29196 Z= 0.318 Chirality : 0.044 0.222 3782 Planarity : 0.004 0.045 3706 Dihedral : 5.356 57.726 3280 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 4.64 % Allowed : 24.12 % Favored : 71.24 % 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: -0.95 (0.15), residues: 3148 helix: 1.24 (0.15), residues: 1312 sheet: -1.34 (0.27), residues: 368 loop : -2.28 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 584 HIS 0.004 0.001 HIS A 801 PHE 0.018 0.002 PHE C 579 TYR 0.012 0.001 TYR A 599 ARG 0.004 0.000 ARG C 716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 253 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7776 (pt) cc_final: 0.7474 (tp) REVERT: A 526 LEU cc_start: 0.8245 (pp) cc_final: 0.8030 (pp) REVERT: A 776 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7127 (mmm-85) REVERT: A 783 MET cc_start: 0.7902 (tpp) cc_final: 0.7506 (ttm) REVERT: B 186 ILE cc_start: 0.9049 (pt) cc_final: 0.8690 (tp) REVERT: B 240 ILE cc_start: 0.8092 (tp) cc_final: 0.7833 (mt) REVERT: B 357 GLN cc_start: 0.7457 (mt0) cc_final: 0.6715 (pp30) REVERT: B 405 HIS cc_start: 0.6888 (t70) cc_final: 0.6597 (t70) REVERT: B 467 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8199 (mptt) REVERT: B 497 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7835 (mtt) REVERT: C 767 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9147 (pp) REVERT: C 775 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: C 783 MET cc_start: 0.7981 (tpp) cc_final: 0.7678 (ttm) REVERT: D 357 GLN cc_start: 0.7213 (mt0) cc_final: 0.6755 (pp30) REVERT: D 467 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8200 (mptt) REVERT: D 901 GLU cc_start: 0.4424 (mm-30) cc_final: 0.4154 (mm-30) outliers start: 79 outliers final: 73 residues processed: 316 average time/residue: 0.2618 time to fit residues: 139.8813 Evaluate side-chains 319 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 243 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 110 optimal weight: 0.0470 chunk 183 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 697 ASN C 162 HIS D 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.181172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152760 restraints weight = 45359.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.147514 restraints weight = 59058.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.146635 restraints weight = 51596.674| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21156 Z= 0.210 Angle : 0.601 11.696 29196 Z= 0.304 Chirality : 0.043 0.214 3782 Planarity : 0.004 0.046 3706 Dihedral : 5.157 58.342 3280 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 5.16 % Allowed : 23.59 % Favored : 71.24 % 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: -0.79 (0.15), residues: 3148 helix: 1.39 (0.15), residues: 1308 sheet: -1.43 (0.26), residues: 392 loop : -2.15 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 789 HIS 0.004 0.001 HIS A 801 PHE 0.020 0.002 PHE D 99 TYR 0.012 0.001 TYR B 239 ARG 0.002 0.000 ARG D 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6214.78 seconds wall clock time: 112 minutes 0.29 seconds (6720.29 seconds total)