Starting phenix.real_space_refine on Wed May 21 03:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ari_43783/05_2025/9ari_43783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ari_43783/05_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_43783/05_2025/9ari_43783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ari_43783/05_2025/9ari_43783.map" model { file = "/net/cci-nas-00/data/ceres_data/9ari_43783/05_2025/9ari_43783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ari_43783/05_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-5687/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: 12.74, per 1000 atoms: 0.61 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: 5.34 Conformation dependent library (CDL) restraints added in 3.0 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: 2.90 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: 7.27 Time building geometry restraints manager: 6.06 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: 0.11 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 47.920 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.860 ------------------------------------------------------------------------------- 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 : 0.010 0.721 21174 Z= 0.610 Angle : 1.161 29.798 29232 Z= 0.754 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 Details of bonding type rmsd hydrogen bonds : bond 0.15092 ( 1036) hydrogen bonds : angle 6.74552 ( 3048) SS BOND : bond 0.25578 ( 18) SS BOND : angle 8.47346 ( 36) covalent geometry : bond 0.00690 (21156) covalent geometry : angle 1.12312 (29196) *********************** 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 : 1.825 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: 0.2519 time to fit residues: 235.2554 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 : 2.212 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.179344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.145588 restraints weight = 43945.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.136355 restraints weight = 57014.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133419 restraints weight = 45353.893| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21174 Z= 0.129 Angle : 0.602 7.532 29232 Z= 0.314 Chirality : 0.043 0.222 3782 Planarity : 0.004 0.052 3706 Dihedral : 7.073 75.254 3365 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 7.04 % Allowed : 16.20 % Favored : 76.76 % 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: -2.13 (0.14), residues: 3148 helix: 0.44 (0.14), residues: 1336 sheet: -2.70 (0.22), residues: 422 loop : -2.93 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 494 HIS 0.005 0.001 HIS B 486 PHE 0.032 0.002 PHE A 575 TYR 0.018 0.001 TYR C 599 ARG 0.008 0.001 ARG C 743 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 1036) hydrogen bonds : angle 4.73616 ( 3048) SS BOND : bond 0.00900 ( 18) SS BOND : angle 0.98683 ( 36) covalent geometry : bond 0.00287 (21156) covalent geometry : angle 0.60131 (29196) *********************** 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: 120 poor density : 318 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7938 (ttm-80) REVERT: A 775 PHE cc_start: 0.7830 (t80) cc_final: 0.7602 (t80) REVERT: A 801 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8339 (t-90) REVERT: B 186 ILE cc_start: 0.9174 (pt) cc_final: 0.8875 (tp) REVERT: B 232 CYS cc_start: 0.6261 (t) cc_final: 0.5607 (t) REVERT: B 240 ILE cc_start: 0.8204 (tp) cc_final: 0.7948 (mt) REVERT: B 357 GLN cc_start: 0.7251 (mt0) cc_final: 0.6290 (pp30) REVERT: B 429 CYS cc_start: 0.4692 (OUTLIER) cc_final: 0.4314 (t) REVERT: B 467 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8229 (mptt) REVERT: B 476 TYR cc_start: 0.7995 (p90) cc_final: 0.7565 (p90) REVERT: B 782 GLN cc_start: 0.8459 (pp30) cc_final: 0.8233 (tm-30) REVERT: C 797 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7701 (pt) REVERT: C 801 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8169 (t-90) REVERT: D 99 PHE cc_start: 0.6282 (t80) cc_final: 0.5971 (t80) REVERT: D 433 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8059 (t) REVERT: D 467 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8228 (mptt) REVERT: D 709 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7263 (t80) REVERT: D 795 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9291 (tp) outliers start: 120 outliers final: 62 residues processed: 414 average time/residue: 0.2556 time to fit residues: 176.3653 Evaluate side-chains 350 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 2.350 ------------------------------------------------------------------------------- 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 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 767 LEU Chi-restraints excluded: chain A residue 773 LEU 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 367 LEU 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 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 710 VAL 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 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 609 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 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: 6.9990 chunk 118 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 173 optimal weight: 0.0980 chunk 125 optimal weight: 5.9990 chunk 186 optimal weight: 0.0020 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 HIS C 748 HIS D 697 ASN D 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.173713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140703 restraints weight = 43478.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.133674 restraints weight = 57964.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.132495 restraints weight = 56216.100| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 21174 Z= 0.217 Angle : 0.662 8.191 29232 Z= 0.349 Chirality : 0.045 0.251 3782 Planarity : 0.004 0.057 3706 Dihedral : 6.468 73.719 3308 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.81 % Favored : 92.12 % Rotamer: Outliers : 7.57 % Allowed : 17.19 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.82 (0.15), residues: 3148 helix: 0.63 (0.14), residues: 1326 sheet: -2.43 (0.23), residues: 420 loop : -2.71 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 559 HIS 0.006 0.001 HIS B 486 PHE 0.038 0.002 PHE A 579 TYR 0.013 0.001 TYR C 668 ARG 0.005 0.001 ARG C 743 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 1036) hydrogen bonds : angle 4.69751 ( 3048) SS BOND : bond 0.00513 ( 18) SS BOND : angle 0.73281 ( 36) covalent geometry : bond 0.00514 (21156) covalent geometry : angle 0.66200 (29196) *********************** 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 410 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 281 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7748 (pt) cc_final: 0.7286 (tp) REVERT: A 797 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.7677 (pt) REVERT: A 801 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8330 (t-90) REVERT: B 186 ILE cc_start: 0.9037 (pt) cc_final: 0.8681 (tp) REVERT: B 240 ILE cc_start: 0.7949 (tp) cc_final: 0.7687 (mt) REVERT: B 357 GLN cc_start: 0.7521 (mt0) cc_final: 0.7282 (pt0) REVERT: B 467 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8228 (mptt) REVERT: C 91 LEU cc_start: 0.7857 (pt) cc_final: 0.7363 (tp) REVERT: C 748 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8300 (m170) REVERT: C 797 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.7725 (pt) REVERT: C 801 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8311 (t-90) REVERT: D 99 PHE cc_start: 0.6143 (t80) cc_final: 0.5710 (t80) REVERT: D 357 GLN cc_start: 0.7827 (mt0) cc_final: 0.7319 (pp30) REVERT: D 433 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8045 (t) REVERT: D 739 MET cc_start: 0.6933 (mtt) cc_final: 0.6721 (mtt) REVERT: D 795 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9246 (tt) outliers start: 129 outliers final: 88 residues processed: 385 average time/residue: 0.2829 time to fit residues: 182.5279 Evaluate side-chains 356 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 261 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR 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 497 VAL 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 714 PHE 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 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 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 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 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 641 ILE 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 C residue 141 VAL Chi-restraints excluded: chain C residue 163 ILE 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 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 677 VAL 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 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 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 482 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 641 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 24 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 50.0000 chunk 134 optimal weight: 0.2980 chunk 272 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 303 optimal weight: 0.7980 chunk 242 optimal weight: 9.9990 chunk 239 optimal weight: 40.0000 chunk 69 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 697 ASN C 748 HIS D 184 ASN D 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.175194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.143618 restraints weight = 44089.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137456 restraints weight = 58355.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135182 restraints weight = 50907.536| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21174 Z= 0.153 Angle : 0.604 8.304 29232 Z= 0.312 Chirality : 0.043 0.202 3782 Planarity : 0.004 0.049 3706 Dihedral : 6.204 71.471 3302 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 8.10 % Allowed : 17.84 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.52 (0.15), residues: 3148 helix: 0.91 (0.14), residues: 1328 sheet: -2.34 (0.23), residues: 428 loop : -2.55 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.017 0.001 HIS C 748 PHE 0.024 0.002 PHE A 579 TYR 0.010 0.001 TYR A 599 ARG 0.002 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 1036) hydrogen bonds : angle 4.38895 ( 3048) SS BOND : bond 0.00373 ( 18) SS BOND : angle 0.71187 ( 36) covalent geometry : bond 0.00354 (21156) covalent geometry : angle 0.60406 (29196) *********************** 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 415 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 277 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7554 (pt) cc_final: 0.7203 (tp) REVERT: A 797 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 801 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8346 (t-90) REVERT: B 186 ILE cc_start: 0.8938 (pt) cc_final: 0.8610 (tp) REVERT: B 240 ILE cc_start: 0.7858 (tp) cc_final: 0.7603 (mt) REVERT: B 357 GLN cc_start: 0.7376 (mt0) cc_final: 0.6502 (pp30) REVERT: B 433 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8008 (t) REVERT: B 467 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8127 (mmtm) REVERT: C 26 ILE cc_start: 0.4067 (OUTLIER) cc_final: 0.3781 (mm) REVERT: C 91 LEU cc_start: 0.7637 (pt) cc_final: 0.7316 (tp) REVERT: C 801 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.8261 (t-90) REVERT: D 99 PHE cc_start: 0.6106 (t80) cc_final: 0.5775 (t80) REVERT: D 357 GLN cc_start: 0.7677 (mt0) cc_final: 0.7336 (pp30) REVERT: D 433 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7972 (t) REVERT: D 467 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8255 (mptt) REVERT: D 795 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9185 (tt) outliers start: 138 outliers final: 89 residues processed: 392 average time/residue: 0.2548 time to fit residues: 166.4346 Evaluate side-chains 363 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 267 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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 374 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 497 VAL 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 710 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 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 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 641 ILE Chi-restraints excluded: chain B residue 655 ILE 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 748 LEU 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 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 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 567 ILE 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 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 769 THR 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 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 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 697 ASN 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 841 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 138 optimal weight: 0.0070 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 33 optimal weight: 40.0000 chunk 279 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.177515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.148276 restraints weight = 45389.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.143077 restraints weight = 57501.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.139457 restraints weight = 50263.834| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21174 Z= 0.154 Angle : 0.600 9.535 29232 Z= 0.308 Chirality : 0.043 0.196 3782 Planarity : 0.004 0.046 3706 Dihedral : 5.983 66.671 3298 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 8.33 % Allowed : 19.01 % 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: -1.31 (0.15), residues: 3148 helix: 1.05 (0.14), residues: 1326 sheet: -2.13 (0.25), residues: 390 loop : -2.43 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.004 0.001 HIS B 486 PHE 0.023 0.002 PHE A 579 TYR 0.010 0.001 TYR A 599 ARG 0.007 0.001 ARG D 696 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1036) hydrogen bonds : angle 4.30908 ( 3048) SS BOND : bond 0.00363 ( 18) SS BOND : angle 0.69931 ( 36) covalent geometry : bond 0.00359 (21156) covalent geometry : angle 0.60029 (29196) *********************** 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 415 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 273 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4132 (OUTLIER) cc_final: 0.3843 (mm) REVERT: A 91 LEU cc_start: 0.7753 (pt) cc_final: 0.7372 (tp) REVERT: A 587 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 776 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.7190 (mmm-85) REVERT: A 794 SER cc_start: 0.9360 (OUTLIER) cc_final: 0.8973 (t) REVERT: A 797 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 801 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.8314 (t-90) REVERT: B 186 ILE cc_start: 0.9042 (pt) cc_final: 0.8681 (tp) REVERT: B 240 ILE cc_start: 0.7985 (tp) cc_final: 0.7731 (mt) REVERT: B 357 GLN cc_start: 0.7358 (mt0) cc_final: 0.6535 (pp30) REVERT: B 467 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8268 (mptt) REVERT: B 663 VAL cc_start: 0.6073 (OUTLIER) cc_final: 0.5862 (p) REVERT: C 26 ILE cc_start: 0.4181 (OUTLIER) cc_final: 0.3942 (mm) REVERT: C 91 LEU cc_start: 0.7769 (pt) cc_final: 0.7427 (tp) REVERT: C 587 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7689 (p) REVERT: C 783 MET cc_start: 0.8157 (tpp) cc_final: 0.7814 (ttm) REVERT: C 801 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.8298 (t-90) REVERT: D 99 PHE cc_start: 0.6323 (t80) cc_final: 0.6009 (t80) REVERT: D 357 GLN cc_start: 0.7596 (mt0) cc_final: 0.7273 (pp30) REVERT: D 433 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8024 (t) REVERT: D 467 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8294 (mptt) REVERT: D 795 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9206 (tt) outliers start: 142 outliers final: 100 residues processed: 396 average time/residue: 0.2490 time to fit residues: 166.1242 Evaluate side-chains 364 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 253 time to evaluate : 2.247 ------------------------------------------------------------------------------- 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 383 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 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 535 VAL 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 587 VAL 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 769 THR Chi-restraints excluded: chain A residue 770 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 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 462 ILE 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 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 641 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 748 LEU 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 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 422 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 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 587 VAL 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 769 THR Chi-restraints excluded: chain C residue 773 LEU 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 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 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 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: 0.6980 chunk 20 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 272 optimal weight: 40.0000 chunk 246 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 235 optimal weight: 0.9990 chunk 189 optimal weight: 40.0000 chunk 221 optimal weight: 0.0970 chunk 140 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.179990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.151126 restraints weight = 45247.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.145995 restraints weight = 54819.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.144182 restraints weight = 52861.028| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21174 Z= 0.107 Angle : 0.567 8.863 29232 Z= 0.286 Chirality : 0.042 0.162 3782 Planarity : 0.003 0.045 3706 Dihedral : 5.646 59.146 3298 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.57 % Allowed : 20.66 % Favored : 72.77 % 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: -1.03 (0.15), residues: 3148 helix: 1.30 (0.15), residues: 1320 sheet: -1.91 (0.25), residues: 408 loop : -2.31 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS B 486 PHE 0.017 0.001 PHE A 579 TYR 0.010 0.001 TYR B 239 ARG 0.002 0.000 ARG A 776 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 1036) hydrogen bonds : angle 4.08791 ( 3048) SS BOND : bond 0.00287 ( 18) SS BOND : angle 0.64403 ( 36) covalent geometry : bond 0.00233 (21156) covalent geometry : angle 0.56652 (29196) *********************** 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 388 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 276 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4012 (OUTLIER) cc_final: 0.3788 (mm) REVERT: A 91 LEU cc_start: 0.7253 (pt) cc_final: 0.6958 (tp) REVERT: A 534 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8493 (mm) REVERT: A 587 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7585 (p) REVERT: A 776 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7252 (mmm-85) REVERT: B 186 ILE cc_start: 0.8883 (pt) cc_final: 0.8513 (tp) REVERT: B 240 ILE cc_start: 0.7720 (tp) cc_final: 0.7481 (mt) REVERT: B 357 GLN cc_start: 0.7225 (mt0) cc_final: 0.6530 (pp30) REVERT: B 405 HIS cc_start: 0.6840 (t70) cc_final: 0.6506 (t70) REVERT: B 433 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7970 (t) REVERT: B 467 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8300 (mptt) REVERT: C 419 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8121 (mt) REVERT: C 775 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: C 783 MET cc_start: 0.8011 (tpp) cc_final: 0.7505 (ttm) REVERT: D 99 PHE cc_start: 0.6026 (t80) cc_final: 0.5724 (t80) REVERT: D 357 GLN cc_start: 0.7216 (mt0) cc_final: 0.6821 (pp30) REVERT: D 433 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8099 (t) REVERT: D 467 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8214 (mptt) REVERT: D 702 MET cc_start: 0.6220 (mmt) cc_final: 0.5930 (mmt) REVERT: D 795 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9155 (tt) outliers start: 112 outliers final: 77 residues processed: 366 average time/residue: 0.2540 time to fit residues: 155.6032 Evaluate side-chains 343 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 258 time to evaluate : 2.158 ------------------------------------------------------------------------------- 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 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 585 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 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 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 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 643 LEU 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 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 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 419 LEU 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 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 636 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 773 LEU 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 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 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 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 841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 282 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 262 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 287 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 243 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.173876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.145230 restraints weight = 45067.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141485 restraints weight = 55842.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137355 restraints weight = 63129.016| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 21174 Z= 0.291 Angle : 0.719 9.353 29232 Z= 0.377 Chirality : 0.047 0.226 3782 Planarity : 0.004 0.045 3706 Dihedral : 5.715 58.201 3281 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.40 % Favored : 90.50 % Rotamer: Outliers : 7.69 % Allowed : 20.19 % 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: -1.31 (0.15), residues: 3148 helix: 0.98 (0.14), residues: 1322 sheet: -1.83 (0.25), residues: 392 loop : -2.45 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 559 HIS 0.011 0.002 HIS A 801 PHE 0.035 0.002 PHE C 554 TYR 0.016 0.002 TYR A 668 ARG 0.005 0.001 ARG D 774 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 1036) hydrogen bonds : angle 4.62425 ( 3048) SS BOND : bond 0.00497 ( 18) SS BOND : angle 1.47561 ( 36) covalent geometry : bond 0.00683 (21156) covalent geometry : angle 0.71743 (29196) *********************** 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 381 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 250 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.3766 (OUTLIER) cc_final: 0.3559 (mm) REVERT: A 91 LEU cc_start: 0.7341 (pt) cc_final: 0.7055 (tp) REVERT: A 241 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9038 (mt) REVERT: A 587 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7847 (p) REVERT: A 776 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7429 (mmm-85) REVERT: B 186 ILE cc_start: 0.8827 (pt) cc_final: 0.8493 (tp) REVERT: B 240 ILE cc_start: 0.7867 (tp) cc_final: 0.7606 (mt) REVERT: B 357 GLN cc_start: 0.7292 (mt0) cc_final: 0.6760 (pp30) REVERT: B 433 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8122 (t) REVERT: B 467 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8291 (mptt) REVERT: C 587 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7817 (p) REVERT: D 433 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8020 (t) REVERT: D 467 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8296 (mptt) REVERT: D 702 MET cc_start: 0.6280 (mmt) cc_final: 0.6021 (mmt) REVERT: D 795 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9196 (tt) outliers start: 131 outliers final: 99 residues processed: 362 average time/residue: 0.2367 time to fit residues: 145.1290 Evaluate side-chains 345 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 239 time to evaluate : 2.072 ------------------------------------------------------------------------------- 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 241 ILE 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 497 VAL 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 587 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TRP 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 770 THR Chi-restraints excluded: chain A residue 794 SER 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 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 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 748 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 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 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 587 VAL 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 769 THR Chi-restraints excluded: chain C residue 793 VAL 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 289 LEU 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 440 ILE Chi-restraints excluded: chain D residue 462 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 224 optimal weight: 9.9990 chunk 46 optimal weight: 0.0000 chunk 266 optimal weight: 0.2980 chunk 198 optimal weight: 0.0370 chunk 275 optimal weight: 0.6980 chunk 16 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 209 optimal weight: 0.5980 overall best weight: 0.3262 ------------------------------------------------------------------------------- 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 = 0.4501 r_free = 0.4501 target = 0.184447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.156429 restraints weight = 45394.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.151185 restraints weight = 51442.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.148716 restraints weight = 48758.547| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21174 Z= 0.110 Angle : 0.603 12.348 29232 Z= 0.302 Chirality : 0.043 0.211 3782 Planarity : 0.004 0.047 3706 Dihedral : 5.246 57.563 3281 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 5.28 % Allowed : 22.71 % Favored : 72.01 % 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: -0.90 (0.15), residues: 3148 helix: 1.39 (0.15), residues: 1312 sheet: -1.58 (0.27), residues: 370 loop : -2.28 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 584 HIS 0.002 0.001 HIS A 801 PHE 0.026 0.001 PHE D 637 TYR 0.010 0.001 TYR A 599 ARG 0.004 0.000 ARG C 716 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 1036) hydrogen bonds : angle 4.13452 ( 3048) SS BOND : bond 0.00282 ( 18) SS BOND : angle 1.13347 ( 36) covalent geometry : bond 0.00226 (21156) covalent geometry : angle 0.60164 (29196) *********************** 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 352 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 262 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7207 (pt) cc_final: 0.7007 (tp) REVERT: A 241 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (mt) REVERT: A 587 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7528 (p) REVERT: A 776 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7041 (mmm-85) REVERT: B 186 ILE cc_start: 0.8896 (pt) cc_final: 0.8594 (tp) REVERT: B 240 ILE cc_start: 0.7695 (tp) cc_final: 0.7459 (mt) REVERT: B 357 GLN cc_start: 0.7358 (mt0) cc_final: 0.6684 (pp30) REVERT: B 405 HIS cc_start: 0.6647 (t70) cc_final: 0.6301 (t70) REVERT: B 433 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8075 (t) REVERT: B 467 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8207 (mptt) REVERT: C 587 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7588 (p) REVERT: C 775 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: C 783 MET cc_start: 0.8125 (tpp) cc_final: 0.7720 (ttm) REVERT: D 433 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8098 (t) REVERT: D 467 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8068 (mmtm) REVERT: D 671 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6067 (t80) REVERT: D 702 MET cc_start: 0.5968 (mmt) cc_final: 0.5733 (mmt) outliers start: 90 outliers final: 68 residues processed: 334 average time/residue: 0.2611 time to fit residues: 146.7901 Evaluate side-chains 327 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 2.403 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain A residue 372 TYR 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 585 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 794 SER 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 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 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 641 ILE 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 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 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 456 ILE 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 587 VAL 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 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 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 428 THR Chi-restraints excluded: chain D residue 433 THR 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 641 ILE Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 824 MET 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: 5.9990 chunk 221 optimal weight: 0.4980 chunk 303 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 224 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.181065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.153320 restraints weight = 45398.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.147656 restraints weight = 58700.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.145976 restraints weight = 54601.016| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21174 Z= 0.143 Angle : 0.598 9.659 29232 Z= 0.305 Chirality : 0.043 0.177 3782 Planarity : 0.004 0.045 3706 Dihedral : 5.164 57.633 3279 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.16 % Allowed : 22.95 % Favored : 71.89 % 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: -0.86 (0.15), residues: 3148 helix: 1.39 (0.15), residues: 1306 sheet: -1.65 (0.26), residues: 404 loop : -2.19 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 796 HIS 0.005 0.001 HIS A 801 PHE 0.023 0.002 PHE D 99 TYR 0.010 0.001 TYR B 239 ARG 0.004 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1036) hydrogen bonds : angle 4.14958 ( 3048) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.10501 ( 36) covalent geometry : bond 0.00332 (21156) covalent geometry : angle 0.59746 (29196) *********************** 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 338 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 250 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9002 (mt) REVERT: A 587 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7556 (p) REVERT: A 776 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7207 (mmm-85) REVERT: A 783 MET cc_start: 0.8161 (tpp) cc_final: 0.7706 (ttm) REVERT: B 186 ILE cc_start: 0.8802 (pt) cc_final: 0.8508 (tp) REVERT: B 240 ILE cc_start: 0.7725 (tp) cc_final: 0.7482 (mt) REVERT: B 357 GLN cc_start: 0.7276 (mt0) cc_final: 0.6663 (pp30) REVERT: B 405 HIS cc_start: 0.6746 (t70) cc_final: 0.6396 (t70) REVERT: B 433 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8117 (t) REVERT: B 467 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8212 (mptt) REVERT: C 241 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8989 (mt) REVERT: C 775 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: C 783 MET cc_start: 0.8135 (tpp) cc_final: 0.7571 (tpp) REVERT: D 433 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8184 (t) REVERT: D 467 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8203 (mptt) REVERT: D 702 MET cc_start: 0.6069 (mmt) cc_final: 0.5852 (mmt) outliers start: 88 outliers final: 76 residues processed: 325 average time/residue: 0.2406 time to fit residues: 132.8369 Evaluate side-chains 330 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 248 time to evaluate : 2.136 ------------------------------------------------------------------------------- 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 241 ILE 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 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 585 LEU Chi-restraints excluded: chain A residue 587 VAL 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 769 THR Chi-restraints excluded: chain A residue 794 SER 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 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 LEU 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 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 241 ILE 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 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 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 793 VAL 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 433 THR 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 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 824 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: 0.2980 chunk 281 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 69 optimal weight: 0.3980 chunk 111 optimal weight: 50.0000 chunk 273 optimal weight: 20.0000 chunk 277 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.184062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.156066 restraints weight = 45586.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.151656 restraints weight = 53061.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.150189 restraints weight = 47756.836| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21174 Z= 0.103 Angle : 0.569 10.638 29232 Z= 0.285 Chirality : 0.042 0.190 3782 Planarity : 0.004 0.047 3706 Dihedral : 4.991 56.616 3279 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.75 % Allowed : 23.18 % Favored : 72.07 % 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: -0.65 (0.16), residues: 3148 helix: 1.59 (0.15), residues: 1310 sheet: -1.56 (0.26), residues: 394 loop : -2.11 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 657 HIS 0.002 0.001 HIS A 592 PHE 0.026 0.001 PHE D 637 TYR 0.011 0.001 TYR B 239 ARG 0.003 0.000 ARG C 716 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 1036) hydrogen bonds : angle 3.95610 ( 3048) SS BOND : bond 0.00252 ( 18) SS BOND : angle 1.06399 ( 36) covalent geometry : bond 0.00221 (21156) covalent geometry : angle 0.56783 (29196) ********************** 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 341 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 260 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8979 (mt) REVERT: A 587 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7165 (p) REVERT: A 776 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.6921 (mmm-85) REVERT: A 783 MET cc_start: 0.7913 (tpp) cc_final: 0.7553 (ttm) REVERT: B 186 ILE cc_start: 0.8813 (pt) cc_final: 0.8457 (tp) REVERT: B 240 ILE cc_start: 0.7647 (tp) cc_final: 0.7412 (mt) REVERT: B 405 HIS cc_start: 0.6635 (t70) cc_final: 0.6381 (t70) REVERT: B 433 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8152 (t) REVERT: B 467 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8143 (mmtm) REVERT: B 476 TYR cc_start: 0.7641 (p90) cc_final: 0.7280 (p90) REVERT: C 241 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8973 (mt) REVERT: C 775 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: D 99 PHE cc_start: 0.5509 (t80) cc_final: 0.5087 (t80) REVERT: D 467 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8203 (mptt) REVERT: D 784 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7282 (t80) outliers start: 81 outliers final: 68 residues processed: 326 average time/residue: 0.2650 time to fit residues: 145.9496 Evaluate side-chains 323 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 249 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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 241 ILE 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 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 587 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 794 SER 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 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 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 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 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 241 ILE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 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 507 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 634 VAL Chi-restraints excluded: chain C residue 710 VAL 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 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 428 THR 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 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 783 LEU Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 824 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 110 optimal weight: 0.1980 chunk 183 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 258 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.0670 chunk 187 optimal weight: 7.9990 overall best weight: 0.4520 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.183968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.155926 restraints weight = 45559.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.151000 restraints weight = 51931.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149414 restraints weight = 50477.870| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21174 Z= 0.102 Angle : 0.573 9.819 29232 Z= 0.285 Chirality : 0.042 0.182 3782 Planarity : 0.004 0.047 3706 Dihedral : 4.789 56.907 3276 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.34 % Allowed : 23.83 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.16), residues: 3148 helix: 1.63 (0.15), residues: 1318 sheet: -1.44 (0.27), residues: 388 loop : -2.06 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 657 HIS 0.002 0.000 HIS B 486 PHE 0.024 0.001 PHE D 637 TYR 0.011 0.001 TYR B 239 ARG 0.003 0.000 ARG C 716 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 1036) hydrogen bonds : angle 3.91087 ( 3048) SS BOND : bond 0.00244 ( 18) SS BOND : angle 1.47888 ( 36) covalent geometry : bond 0.00221 (21156) covalent geometry : angle 0.57073 (29196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.04 seconds wall clock time: 111 minutes 52.99 seconds (6712.99 seconds total)