Starting phenix.real_space_refine on Sun May 18 00:52:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tr3_41569/05_2025/8tr3_41569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tr3_41569/05_2025/8tr3_41569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tr3_41569/05_2025/8tr3_41569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tr3_41569/05_2025/8tr3_41569.map" model { file = "/net/cci-nas-00/data/ceres_data/8tr3_41569/05_2025/8tr3_41569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tr3_41569/05_2025/8tr3_41569.cif" } resolution = 3.74 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= 0.001 sd= 0.040 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 99 5.16 5 C 10305 2.51 5 N 2763 2.21 5 O 3234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16401 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 16, 'TRANS': 295} Chain breaks: 5 Chain: "B" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 16, 'TRANS': 295} Chain breaks: 5 Chain: "D" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "M" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 16, 'TRANS': 295} Chain breaks: 5 Chain: "F" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.83, per 1000 atoms: 0.60 Number of scatterers: 16401 At special positions: 0 Unit cell: (147.396, 139.728, 99.684, 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 99 16.00 O 3234 8.00 N 2763 7.00 C 10305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " " NAG c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " " NAG p 1 " - " NAG p 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 230 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 363 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 413 " " NAG A 609 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 230 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 363 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 392 " " NAG C 608 " - " ASN C 413 " " NAG C 609 " - " ASN C 448 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 230 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 363 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 392 " " NAG E 608 " - " ASN E 413 " " NAG E 609 " - " ASN E 448 " " NAG P 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG c 1 " - " ASN C 241 " " NAG e 1 " - " ASN C 262 " " NAG p 1 " - " ASN E 241 " " NAG r 1 " - " ASN E 262 " Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 2.0 seconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3756 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 30 sheets defined 23.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.609A pdb=" N PHE A 391 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.696A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 removed outlier: 4.363A pdb=" N PHE B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.852A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 Processing helix chain 'B' and resid 562 through 596 removed outlier: 3.557A pdb=" N GLN B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 568 " --> pdb=" O HIS B 564 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.672A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 655 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.290A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.958A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.609A pdb=" N PHE C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.697A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 522 removed outlier: 4.363A pdb=" N PHE D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 removed outlier: 3.851A pdb=" N ILE D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 546 Processing helix chain 'D' and resid 562 through 596 removed outlier: 3.557A pdb=" N GLN D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR D 569 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.671A pdb=" N ILE D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 655 Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.291A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.958A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.609A pdb=" N PHE E 391 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.696A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 522 removed outlier: 4.363A pdb=" N PHE F 519 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU F 520 " --> pdb=" O GLY F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.852A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 546 Processing helix chain 'F' and resid 562 through 596 removed outlier: 3.557A pdb=" N GLN F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 568 " --> pdb=" O HIS F 564 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR F 569 " --> pdb=" O LEU F 565 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F 570 " --> pdb=" O LEU F 566 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.672A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 655 Processing helix chain 'J' and resid 28 through 31 Processing helix chain 'J' and resid 83 through 87 removed outlier: 4.290A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.959A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.504A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 244 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.509A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 334 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.686A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.102A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.504A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 244 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'C' and resid 260 through 261 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.509A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C 334 " --> pdb=" O ASN C 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 374 through 377 Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.686A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'M' and resid 10 through 14 removed outlier: 6.103A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS M 107 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA M 13 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA M 84 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.504A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 244 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC6, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.508A pdb=" N CYS E 445 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER E 334 " --> pdb=" O ASN E 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 374 through 377 Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.686A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.103A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA N 13 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1647 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: 5.75 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5199 1.34 - 1.47: 4265 1.47 - 1.59: 7126 1.59 - 1.72: 3 1.72 - 1.85: 138 Bond restraints: 16731 Sorted by residual: bond pdb=" CD GLN I 6 " pdb=" NE2 GLN I 6 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.47e+01 bond pdb=" CD GLN H 6 " pdb=" NE2 GLN H 6 " ideal model delta sigma weight residual 1.328 1.248 0.080 2.10e-02 2.27e+03 1.45e+01 bond pdb=" CD GLN J 6 " pdb=" NE2 GLN J 6 " ideal model delta sigma weight residual 1.328 1.249 0.079 2.10e-02 2.27e+03 1.43e+01 bond pdb=" CD GLN J 1 " pdb=" NE2 GLN J 1 " ideal model delta sigma weight residual 1.328 1.250 0.078 2.10e-02 2.27e+03 1.38e+01 bond pdb=" CD GLN I 1 " pdb=" NE2 GLN I 1 " ideal model delta sigma weight residual 1.328 1.250 0.078 2.10e-02 2.27e+03 1.38e+01 ... (remaining 16726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 22096 1.95 - 3.90: 526 3.90 - 5.85: 76 5.85 - 7.80: 18 7.80 - 9.76: 6 Bond angle restraints: 22722 Sorted by residual: angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 106.43 5.57 1.40e+00 5.10e-01 1.58e+01 angle pdb=" CA PRO N 8 " pdb=" N PRO N 8 " pdb=" CD PRO N 8 " ideal model delta sigma weight residual 112.00 106.51 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA PRO M 8 " pdb=" N PRO M 8 " pdb=" CD PRO M 8 " ideal model delta sigma weight residual 112.00 106.52 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" CA GLN N 3 " pdb=" CB GLN N 3 " pdb=" CG GLN N 3 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA GLN L 3 " pdb=" CB GLN L 3 " pdb=" CG GLN L 3 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 ... (remaining 22717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 8902 16.75 - 33.51: 1198 33.51 - 50.26: 262 50.26 - 67.02: 81 67.02 - 83.77: 30 Dihedral angle restraints: 10473 sinusoidal: 4647 harmonic: 5826 Sorted by residual: dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -152.30 66.30 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual -86.00 -152.28 66.28 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -152.27 66.27 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 10470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2180 0.056 - 0.113: 441 0.113 - 0.169: 55 0.169 - 0.225: 3 0.225 - 0.282: 3 Chirality restraints: 2682 Sorted by residual: chirality pdb=" C1 NAG p 1 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG p 1 " pdb=" O5 NAG p 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2679 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 45 " 0.019 2.00e-02 2.50e+03 1.61e-02 6.50e+00 pdb=" CG TRP E 45 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 45 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 45 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 45 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 45 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 45 " 0.019 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP C 45 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 45 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 45 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 45 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 45 " 0.019 2.00e-02 2.50e+03 1.59e-02 6.34e+00 pdb=" CG TRP A 45 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 45 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 45 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 45 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 45 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 45 " 0.003 2.00e-02 2.50e+03 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3045 2.77 - 3.31: 15160 3.31 - 3.84: 26190 3.84 - 4.37: 28354 4.37 - 4.90: 50488 Nonbonded interactions: 123237 Sorted by model distance: nonbonded pdb=" O SER D 546 " pdb=" OG SER D 546 " model vdw 2.243 3.040 nonbonded pdb=" O SER B 546 " pdb=" OG SER B 546 " model vdw 2.243 3.040 nonbonded pdb=" O SER F 546 " pdb=" OG SER F 546 " model vdw 2.244 3.040 nonbonded pdb=" O ALA L 13 " pdb=" N LYS L 107 " model vdw 2.260 3.120 nonbonded pdb=" O ALA N 13 " pdb=" N LYS N 107 " model vdw 2.261 3.120 ... (remaining 123232 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'c' selection = chain 'e' selection = chain 'p' selection = chain 'r' } 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=0.00 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: 3.470 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.870 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.005 0.111 16800 Z= 0.200 Angle : 0.731 9.756 22899 Z= 0.366 Chirality : 0.047 0.282 2682 Planarity : 0.004 0.041 2820 Dihedral : 16.049 83.772 6627 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.34 % Allowed : 25.47 % Favored : 74.19 % 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: -0.94 (0.20), residues: 1968 helix: 1.69 (0.28), residues: 396 sheet: -0.20 (0.20), residues: 678 loop : -2.09 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 45 HIS 0.004 0.001 HIS I 97 PHE 0.013 0.001 PHE J 29 TYR 0.008 0.001 TYR C 40 ARG 0.007 0.001 ARG D 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 33) link_NAG-ASN : angle 1.67611 ( 99) link_BETA1-4 : bond 0.00597 ( 6) link_BETA1-4 : angle 1.56798 ( 18) hydrogen bonds : bond 0.10642 ( 612) hydrogen bonds : angle 5.78374 ( 1647) SS BOND : bond 0.00614 ( 30) SS BOND : angle 1.51041 ( 60) covalent geometry : bond 0.00466 (16731) covalent geometry : angle 0.71973 (22722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 263 time to evaluate : 1.920 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: I 46 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7388 (mt-10) REVERT: N 105 GLU cc_start: 0.6753 (mp0) cc_final: 0.6395 (tm-30) outliers start: 6 outliers final: 3 residues processed: 263 average time/residue: 0.3293 time to fit residues: 122.4818 Evaluate side-chains 234 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain E residue 280 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 343 GLN A 404 GLN A 442 GLN A 463 ASN B 577 GLN H 97 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 343 GLN C 404 GLN C 442 GLN C 463 ASN D 577 GLN I 97 HIS ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN E 343 GLN E 404 GLN E 442 GLN E 463 ASN F 577 GLN J 97 HIS ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.128999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092637 restraints weight = 37113.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092537 restraints weight = 27806.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093500 restraints weight = 23103.210| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16800 Z= 0.239 Angle : 0.721 7.009 22899 Z= 0.368 Chirality : 0.047 0.189 2682 Planarity : 0.004 0.036 2820 Dihedral : 6.909 49.794 2973 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.34 % Allowed : 23.43 % Favored : 73.23 % 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: -1.21 (0.19), residues: 1968 helix: 1.38 (0.26), residues: 399 sheet: -0.25 (0.20), residues: 660 loop : -2.32 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 36 HIS 0.007 0.002 HIS E 374 PHE 0.016 0.002 PHE E 376 TYR 0.016 0.002 TYR C 486 ARG 0.006 0.001 ARG I 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 33) link_NAG-ASN : angle 1.74736 ( 99) link_BETA1-4 : bond 0.00329 ( 6) link_BETA1-4 : angle 0.89819 ( 18) hydrogen bonds : bond 0.04503 ( 612) hydrogen bonds : angle 5.30396 ( 1647) SS BOND : bond 0.00832 ( 30) SS BOND : angle 1.50554 ( 60) covalent geometry : bond 0.00573 (16731) covalent geometry : angle 0.70979 (22722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 261 time to evaluate : 1.678 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: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.7324 (m100) REVERT: B 530 MET cc_start: 0.7530 (mtt) cc_final: 0.7014 (mtt) REVERT: H 38 ARG cc_start: 0.8391 (ptt180) cc_final: 0.8050 (ptt90) REVERT: H 46 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7328 (mt-10) REVERT: H 48 MET cc_start: 0.8189 (mmm) cc_final: 0.7731 (mmm) REVERT: H 66 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8309 (mtm-85) REVERT: L 105 GLU cc_start: 0.7091 (mp0) cc_final: 0.6888 (tm-30) REVERT: C 479 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.6454 (m100) REVERT: D 587 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8958 (mm) REVERT: I 46 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7397 (mt-10) REVERT: M 103 LYS cc_start: 0.8562 (tppt) cc_final: 0.8179 (tptp) REVERT: E 398 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6928 (p0) REVERT: E 479 TRP cc_start: 0.8380 (OUTLIER) cc_final: 0.6564 (m100) REVERT: F 522 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7801 (t80) REVERT: J 38 ARG cc_start: 0.8400 (ptt180) cc_final: 0.8146 (ptt90) REVERT: J 46 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7566 (mt-10) REVERT: N 105 GLU cc_start: 0.7074 (mp0) cc_final: 0.6775 (tm-30) outliers start: 59 outliers final: 30 residues processed: 297 average time/residue: 0.3042 time to fit residues: 129.6611 Evaluate side-chains 265 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain J residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 124 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 157 optimal weight: 0.2980 chunk 82 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.130882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093144 restraints weight = 36868.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093450 restraints weight = 25041.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094548 restraints weight = 20878.178| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16800 Z= 0.133 Angle : 0.633 8.569 22899 Z= 0.322 Chirality : 0.045 0.204 2682 Planarity : 0.003 0.042 2820 Dihedral : 6.102 42.013 2967 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.77 % Allowed : 25.47 % Favored : 71.76 % 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: -1.04 (0.19), residues: 1968 helix: 1.69 (0.27), residues: 399 sheet: -0.22 (0.20), residues: 672 loop : -2.25 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.003 0.001 HIS E 374 PHE 0.015 0.001 PHE E 376 TYR 0.015 0.001 TYR I 59 ARG 0.005 0.001 ARG E 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 33) link_NAG-ASN : angle 1.70298 ( 99) link_BETA1-4 : bond 0.00325 ( 6) link_BETA1-4 : angle 0.89088 ( 18) hydrogen bonds : bond 0.03878 ( 612) hydrogen bonds : angle 5.12704 ( 1647) SS BOND : bond 0.00672 ( 30) SS BOND : angle 1.32507 ( 60) covalent geometry : bond 0.00316 (16731) covalent geometry : angle 0.62116 (22722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.827 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: symmetry clash REVERT: B 530 MET cc_start: 0.7613 (mtt) cc_final: 0.7102 (mtt) REVERT: H 46 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7308 (mt-10) REVERT: L 103 LYS cc_start: 0.8339 (tptp) cc_final: 0.8037 (tptp) REVERT: C 114 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8114 (tm-30) REVERT: I 46 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7335 (mt-10) REVERT: M 105 GLU cc_start: 0.6634 (mp0) cc_final: 0.6283 (tm-30) REVERT: E 398 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6890 (p0) REVERT: F 522 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.8093 (t80) REVERT: J 46 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7384 (mt-10) REVERT: J 48 MET cc_start: 0.8388 (mmm) cc_final: 0.7930 (mmm) REVERT: N 103 LYS cc_start: 0.8303 (tptp) cc_final: 0.7874 (tptp) outliers start: 49 outliers final: 35 residues processed: 291 average time/residue: 0.3104 time to fit residues: 130.1306 Evaluate side-chains 272 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain J residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.130698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092845 restraints weight = 37042.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093258 restraints weight = 25042.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094028 restraints weight = 21368.698| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16800 Z= 0.145 Angle : 0.631 7.970 22899 Z= 0.320 Chirality : 0.045 0.201 2682 Planarity : 0.004 0.043 2820 Dihedral : 5.661 34.422 2967 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.13 % Allowed : 25.35 % Favored : 70.51 % 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 (0.19), residues: 1968 helix: 1.42 (0.27), residues: 417 sheet: -0.16 (0.20), residues: 654 loop : -2.18 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.003 0.001 HIS E 374 PHE 0.015 0.002 PHE E 376 TYR 0.014 0.001 TYR I 59 ARG 0.009 0.001 ARG J 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 33) link_NAG-ASN : angle 1.50500 ( 99) link_BETA1-4 : bond 0.00283 ( 6) link_BETA1-4 : angle 0.86552 ( 18) hydrogen bonds : bond 0.03759 ( 612) hydrogen bonds : angle 5.03729 ( 1647) SS BOND : bond 0.00679 ( 30) SS BOND : angle 1.33616 ( 60) covalent geometry : bond 0.00348 (16731) covalent geometry : angle 0.62107 (22722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 260 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.7155 (m100) REVERT: B 530 MET cc_start: 0.7681 (mtt) cc_final: 0.7258 (mtt) REVERT: H 46 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7219 (mt-10) REVERT: H 48 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7963 (mtm) REVERT: H 66 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8365 (ptm160) REVERT: L 103 LYS cc_start: 0.8412 (tptp) cc_final: 0.7912 (tptp) REVERT: C 479 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.6416 (m100) REVERT: I 46 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7284 (mt-10) REVERT: M 14 SER cc_start: 0.9035 (m) cc_final: 0.8794 (p) REVERT: M 78 LEU cc_start: 0.8332 (mt) cc_final: 0.8118 (mt) REVERT: M 103 LYS cc_start: 0.8221 (tptp) cc_final: 0.7789 (tptp) REVERT: E 389 ASP cc_start: 0.8888 (t70) cc_final: 0.8436 (p0) REVERT: E 390 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8005 (pp) REVERT: E 398 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6928 (p0) REVERT: E 479 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.6598 (m100) REVERT: F 522 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8090 (t80) REVERT: J 38 ARG cc_start: 0.8409 (ptt90) cc_final: 0.7997 (ptm-80) REVERT: J 46 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7417 (mt-10) REVERT: J 48 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7985 (mtm) REVERT: N 105 GLU cc_start: 0.7248 (mp0) cc_final: 0.6979 (tm-30) outliers start: 73 outliers final: 43 residues processed: 311 average time/residue: 0.2853 time to fit residues: 130.3404 Evaluate side-chains 285 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 178 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089917 restraints weight = 37518.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090379 restraints weight = 25547.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091358 restraints weight = 21289.093| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16800 Z= 0.248 Angle : 0.714 8.735 22899 Z= 0.361 Chirality : 0.048 0.267 2682 Planarity : 0.004 0.042 2820 Dihedral : 5.893 37.884 2967 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.04 % Allowed : 24.84 % Favored : 70.12 % 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: -1.18 (0.19), residues: 1968 helix: 1.48 (0.27), residues: 399 sheet: -0.22 (0.20), residues: 654 loop : -2.33 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 338 HIS 0.006 0.001 HIS C 374 PHE 0.015 0.002 PHE E 376 TYR 0.014 0.002 TYR C 486 ARG 0.008 0.001 ARG I 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 33) link_NAG-ASN : angle 2.00918 ( 99) link_BETA1-4 : bond 0.00219 ( 6) link_BETA1-4 : angle 0.89472 ( 18) hydrogen bonds : bond 0.04294 ( 612) hydrogen bonds : angle 5.10490 ( 1647) SS BOND : bond 0.00832 ( 30) SS BOND : angle 1.44914 ( 60) covalent geometry : bond 0.00595 (16731) covalent geometry : angle 0.69988 (22722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 239 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: A 479 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7512 (m100) REVERT: B 530 MET cc_start: 0.7818 (mtt) cc_final: 0.7394 (mtt) REVERT: B 550 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.4615 (pp30) REVERT: H 46 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7256 (mt-10) REVERT: H 48 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: L 62 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: L 105 GLU cc_start: 0.7089 (mp0) cc_final: 0.6771 (tm-30) REVERT: C 103 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: C 398 ASN cc_start: 0.7169 (OUTLIER) cc_final: 0.6846 (p0) REVERT: C 479 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.6504 (m100) REVERT: D 550 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.4538 (pp30) REVERT: I 46 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7325 (mt-10) REVERT: I 66 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8215 (mtm-85) REVERT: M 105 GLU cc_start: 0.6747 (mp0) cc_final: 0.6101 (tm-30) REVERT: E 103 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8821 (tt0) REVERT: E 389 ASP cc_start: 0.8844 (t70) cc_final: 0.8430 (p0) REVERT: E 390 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8127 (pp) REVERT: E 479 TRP cc_start: 0.8427 (OUTLIER) cc_final: 0.6650 (m100) REVERT: F 522 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8109 (t80) REVERT: F 550 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.4548 (pp30) REVERT: J 38 ARG cc_start: 0.8449 (ptt90) cc_final: 0.8078 (ptm-80) REVERT: J 46 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7432 (mt-10) REVERT: J 48 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7944 (mtm) REVERT: N 103 LYS cc_start: 0.8262 (tptp) cc_final: 0.8044 (tptp) outliers start: 89 outliers final: 57 residues processed: 305 average time/residue: 0.2819 time to fit residues: 127.1511 Evaluate side-chains 300 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 188 optimal weight: 0.0770 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.131307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101634 restraints weight = 36816.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101882 restraints weight = 32058.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.102092 restraints weight = 35550.928| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16800 Z= 0.120 Angle : 0.629 8.499 22899 Z= 0.319 Chirality : 0.045 0.209 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.272 34.074 2967 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.30 % Allowed : 25.98 % Favored : 69.72 % 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: -1.08 (0.19), residues: 1968 helix: 1.45 (0.27), residues: 417 sheet: -0.30 (0.20), residues: 681 loop : -2.20 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 112 HIS 0.004 0.001 HIS C 374 PHE 0.015 0.002 PHE N 62 TYR 0.026 0.001 TYR H 59 ARG 0.007 0.001 ARG H 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 33) link_NAG-ASN : angle 1.46838 ( 99) link_BETA1-4 : bond 0.00326 ( 6) link_BETA1-4 : angle 0.88666 ( 18) hydrogen bonds : bond 0.03460 ( 612) hydrogen bonds : angle 4.92253 ( 1647) SS BOND : bond 0.00601 ( 30) SS BOND : angle 1.23578 ( 60) covalent geometry : bond 0.00285 (16731) covalent geometry : angle 0.61987 (22722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 253 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.7199 (m100) REVERT: B 550 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.4603 (pp30) REVERT: H 46 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7121 (mt-10) REVERT: H 48 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7692 (mtm) REVERT: H 59 TYR cc_start: 0.7405 (m-80) cc_final: 0.6812 (m-10) REVERT: L 103 LYS cc_start: 0.8296 (tptp) cc_final: 0.7912 (tptp) REVERT: C 104 MET cc_start: 0.8639 (ttm) cc_final: 0.8083 (ttm) REVERT: C 389 ASP cc_start: 0.8504 (t70) cc_final: 0.8267 (p0) REVERT: C 390 LEU cc_start: 0.8301 (pp) cc_final: 0.8029 (pp) REVERT: C 479 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.6502 (m100) REVERT: D 550 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.4613 (pp30) REVERT: I 46 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7062 (mt-10) REVERT: I 48 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7662 (mtm) REVERT: I 66 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8269 (ptm160) REVERT: M 78 LEU cc_start: 0.8299 (mt) cc_final: 0.8079 (mm) REVERT: M 103 LYS cc_start: 0.7845 (tptp) cc_final: 0.7545 (tptp) REVERT: E 103 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: E 389 ASP cc_start: 0.8725 (t70) cc_final: 0.8399 (p0) REVERT: E 390 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8126 (pp) REVERT: E 479 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.6657 (m100) REVERT: F 522 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7856 (t80) REVERT: F 550 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.4677 (pp30) REVERT: J 38 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8068 (ptm-80) REVERT: J 46 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7315 (mt-10) REVERT: J 48 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7627 (mtm) REVERT: N 78 LEU cc_start: 0.8308 (mt) cc_final: 0.7827 (mt) REVERT: N 103 LYS cc_start: 0.8189 (tptp) cc_final: 0.7894 (tptp) outliers start: 76 outliers final: 44 residues processed: 310 average time/residue: 0.2909 time to fit residues: 133.2507 Evaluate side-chains 288 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 79 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.124777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.087080 restraints weight = 36972.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085853 restraints weight = 24857.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086755 restraints weight = 22091.422| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16800 Z= 0.278 Angle : 0.771 10.401 22899 Z= 0.386 Chirality : 0.049 0.315 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.877 39.866 2967 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.81 % Allowed : 26.54 % Favored : 68.65 % 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: -1.28 (0.19), residues: 1968 helix: 1.41 (0.27), residues: 399 sheet: -0.23 (0.20), residues: 651 loop : -2.43 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 112 HIS 0.006 0.002 HIS C 374 PHE 0.015 0.002 PHE E 376 TYR 0.021 0.002 TYR M 87 ARG 0.008 0.001 ARG I 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 33) link_NAG-ASN : angle 2.39767 ( 99) link_BETA1-4 : bond 0.00306 ( 6) link_BETA1-4 : angle 0.93756 ( 18) hydrogen bonds : bond 0.04447 ( 612) hydrogen bonds : angle 5.08062 ( 1647) SS BOND : bond 0.00861 ( 30) SS BOND : angle 1.50463 ( 60) covalent geometry : bond 0.00666 (16731) covalent geometry : angle 0.75272 (22722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 233 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: A 246 GLN cc_start: 0.8281 (tp40) cc_final: 0.7853 (tp40) REVERT: A 479 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7475 (m100) REVERT: B 550 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.4563 (pp30) REVERT: H 48 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8161 (mtm) REVERT: H 59 TYR cc_start: 0.7503 (m-80) cc_final: 0.7283 (m-10) REVERT: L 103 LYS cc_start: 0.8325 (tptp) cc_final: 0.7903 (tptp) REVERT: C 103 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: C 398 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6761 (p0) REVERT: C 479 TRP cc_start: 0.8489 (OUTLIER) cc_final: 0.6524 (m100) REVERT: D 550 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.4472 (pp30) REVERT: I 38 ARG cc_start: 0.8366 (ptm-80) cc_final: 0.8049 (ptm-80) REVERT: I 46 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7257 (mt-10) REVERT: I 48 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7912 (mtm) REVERT: I 82 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7882 (mpp-170) REVERT: M 103 LYS cc_start: 0.7969 (tptp) cc_final: 0.7640 (tptp) REVERT: E 103 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.8829 (tt0) REVERT: E 389 ASP cc_start: 0.8944 (t70) cc_final: 0.8431 (p0) REVERT: E 390 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8223 (pp) REVERT: E 479 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.6735 (m100) REVERT: F 522 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8176 (t80) REVERT: F 550 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.4692 (pp30) REVERT: J 38 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (ptm-80) REVERT: J 46 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7312 (mt-10) REVERT: J 48 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: J 59 TYR cc_start: 0.7557 (m-10) cc_final: 0.7326 (m-10) REVERT: N 103 LYS cc_start: 0.8337 (tptp) cc_final: 0.7994 (tptp) outliers start: 85 outliers final: 59 residues processed: 292 average time/residue: 0.2785 time to fit residues: 121.0904 Evaluate side-chains 308 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 17 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 56 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN M 38 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN N 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.101802 restraints weight = 36918.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.100406 restraints weight = 31439.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101390 restraints weight = 33853.730| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16800 Z= 0.123 Angle : 0.658 9.706 22899 Z= 0.332 Chirality : 0.045 0.227 2682 Planarity : 0.004 0.045 2820 Dihedral : 5.242 34.695 2967 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.19 % Allowed : 27.45 % Favored : 68.36 % 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: -1.14 (0.19), residues: 1968 helix: 1.41 (0.27), residues: 417 sheet: -0.33 (0.20), residues: 681 loop : -2.25 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 112 HIS 0.004 0.001 HIS C 374 PHE 0.017 0.002 PHE N 62 TYR 0.029 0.001 TYR M 87 ARG 0.006 0.001 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 33) link_NAG-ASN : angle 1.69246 ( 99) link_BETA1-4 : bond 0.00357 ( 6) link_BETA1-4 : angle 0.91093 ( 18) hydrogen bonds : bond 0.03501 ( 612) hydrogen bonds : angle 4.89433 ( 1647) SS BOND : bond 0.00608 ( 30) SS BOND : angle 1.22090 ( 60) covalent geometry : bond 0.00289 (16731) covalent geometry : angle 0.64780 (22722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 1.846 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: symmetry clash REVERT: A 103 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 550 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.4649 (pp30) REVERT: H 46 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7370 (mt-10) REVERT: H 48 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: H 59 TYR cc_start: 0.7500 (m-80) cc_final: 0.7271 (m-10) REVERT: L 78 LEU cc_start: 0.8426 (mt) cc_final: 0.8016 (mt) REVERT: L 103 LYS cc_start: 0.8336 (tptp) cc_final: 0.7846 (tptp) REVERT: C 103 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: C 104 MET cc_start: 0.8650 (ttm) cc_final: 0.7650 (ttm) REVERT: C 389 ASP cc_start: 0.8574 (t70) cc_final: 0.8293 (p0) REVERT: C 479 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.6454 (m100) REVERT: D 550 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.4635 (pp30) REVERT: I 38 ARG cc_start: 0.8285 (ptm-80) cc_final: 0.7877 (ptm-80) REVERT: M 103 LYS cc_start: 0.7829 (tptp) cc_final: 0.7388 (tptp) REVERT: E 103 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8831 (tt0) REVERT: E 479 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.6689 (m100) REVERT: F 522 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7865 (t80) REVERT: F 550 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.4791 (pp30) REVERT: J 46 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7137 (mt-10) REVERT: N 78 LEU cc_start: 0.8484 (mt) cc_final: 0.7923 (mt) REVERT: N 103 LYS cc_start: 0.8299 (tptp) cc_final: 0.7906 (tptp) outliers start: 74 outliers final: 48 residues processed: 297 average time/residue: 0.2912 time to fit residues: 127.5586 Evaluate side-chains 288 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 39 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 68 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 15 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.130641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101154 restraints weight = 36888.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.101123 restraints weight = 32001.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101177 restraints weight = 36489.932| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16800 Z= 0.143 Angle : 0.668 9.698 22899 Z= 0.336 Chirality : 0.045 0.210 2682 Planarity : 0.004 0.045 2820 Dihedral : 5.136 33.326 2967 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.79 % Allowed : 27.67 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.19), residues: 1968 helix: 1.41 (0.27), residues: 417 sheet: -0.29 (0.20), residues: 678 loop : -2.30 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP J 103 HIS 0.005 0.001 HIS C 374 PHE 0.016 0.002 PHE N 62 TYR 0.025 0.001 TYR N 92 ARG 0.008 0.001 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 33) link_NAG-ASN : angle 1.60753 ( 99) link_BETA1-4 : bond 0.00324 ( 6) link_BETA1-4 : angle 0.94238 ( 18) hydrogen bonds : bond 0.03604 ( 612) hydrogen bonds : angle 4.88866 ( 1647) SS BOND : bond 0.00639 ( 30) SS BOND : angle 1.27727 ( 60) covalent geometry : bond 0.00345 (16731) covalent geometry : angle 0.65796 (22722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 530 MET cc_start: 0.7745 (mtt) cc_final: 0.7267 (mtt) REVERT: B 550 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.4712 (pp30) REVERT: H 46 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7336 (mt-10) REVERT: H 48 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7858 (mtm) REVERT: L 62 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: L 79 GLN cc_start: 0.7689 (mp-120) cc_final: 0.7437 (mp10) REVERT: L 105 GLU cc_start: 0.7078 (mp0) cc_final: 0.6776 (tm-30) REVERT: C 103 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: C 104 MET cc_start: 0.8709 (ttm) cc_final: 0.8128 (ttm) REVERT: C 389 ASP cc_start: 0.8583 (t70) cc_final: 0.8305 (p0) REVERT: C 479 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.6525 (m100) REVERT: D 550 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.4691 (pp30) REVERT: M 105 GLU cc_start: 0.6590 (mp0) cc_final: 0.5711 (tm-30) REVERT: E 103 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: E 479 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.6678 (m100) REVERT: F 522 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7900 (t80) REVERT: F 550 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.4813 (pp30) REVERT: J 46 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7072 (mt-10) REVERT: J 48 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7731 (mtm) REVERT: N 105 GLU cc_start: 0.7260 (mp0) cc_final: 0.6946 (tm-30) outliers start: 67 outliers final: 50 residues processed: 281 average time/residue: 0.2879 time to fit residues: 120.6638 Evaluate side-chains 294 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 102 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.131131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100928 restraints weight = 37091.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101854 restraints weight = 35040.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102850 restraints weight = 27922.729| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16800 Z= 0.138 Angle : 0.686 9.473 22899 Z= 0.345 Chirality : 0.045 0.202 2682 Planarity : 0.004 0.045 2820 Dihedral : 5.069 31.987 2967 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.90 % Allowed : 28.01 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 1968 helix: 1.45 (0.27), residues: 417 sheet: -0.30 (0.20), residues: 678 loop : -2.32 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 112 HIS 0.004 0.001 HIS C 374 PHE 0.016 0.002 PHE N 62 TYR 0.020 0.001 TYR M 87 ARG 0.013 0.001 ARG J 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 33) link_NAG-ASN : angle 1.54260 ( 99) link_BETA1-4 : bond 0.00249 ( 6) link_BETA1-4 : angle 0.93260 ( 18) hydrogen bonds : bond 0.03535 ( 612) hydrogen bonds : angle 4.81879 ( 1647) SS BOND : bond 0.00618 ( 30) SS BOND : angle 1.25318 ( 60) covalent geometry : bond 0.00334 (16731) covalent geometry : angle 0.67718 (22722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 234 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: A 479 TRP cc_start: 0.8134 (OUTLIER) cc_final: 0.6990 (m100) REVERT: B 530 MET cc_start: 0.7726 (mtt) cc_final: 0.7266 (mtt) REVERT: B 550 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.4709 (pp30) REVERT: H 46 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7298 (mt-10) REVERT: H 48 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: L 62 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: L 79 GLN cc_start: 0.7749 (mp-120) cc_final: 0.7295 (mp10) REVERT: C 103 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: C 104 MET cc_start: 0.8687 (ttm) cc_final: 0.8077 (ttm) REVERT: C 389 ASP cc_start: 0.8515 (t70) cc_final: 0.8286 (p0) REVERT: C 479 TRP cc_start: 0.8129 (OUTLIER) cc_final: 0.6485 (m100) REVERT: D 550 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.4628 (pp30) REVERT: M 18 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.8039 (ttp80) REVERT: E 103 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8903 (tt0) REVERT: E 479 TRP cc_start: 0.8138 (OUTLIER) cc_final: 0.6655 (m100) REVERT: F 522 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7893 (t80) REVERT: F 550 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.4782 (pp30) REVERT: J 46 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7008 (mt-10) outliers start: 69 outliers final: 52 residues processed: 283 average time/residue: 0.2893 time to fit residues: 121.7353 Evaluate side-chains 286 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 12 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.127629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097232 restraints weight = 37249.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098379 restraints weight = 36848.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099134 restraints weight = 27412.220| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16800 Z= 0.284 Angle : 0.794 13.265 22899 Z= 0.399 Chirality : 0.049 0.223 2682 Planarity : 0.004 0.047 2820 Dihedral : 5.767 40.872 2967 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.96 % Allowed : 27.67 % Favored : 68.36 % 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: -1.40 (0.19), residues: 1968 helix: 1.39 (0.27), residues: 399 sheet: -0.48 (0.20), residues: 657 loop : -2.42 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP J 103 HIS 0.006 0.002 HIS C 374 PHE 0.016 0.002 PHE N 62 TYR 0.023 0.002 TYR N 92 ARG 0.013 0.001 ARG J 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 33) link_NAG-ASN : angle 1.89294 ( 99) link_BETA1-4 : bond 0.00220 ( 6) link_BETA1-4 : angle 0.93802 ( 18) hydrogen bonds : bond 0.04539 ( 612) hydrogen bonds : angle 5.11217 ( 1647) SS BOND : bond 0.00862 ( 30) SS BOND : angle 1.46206 ( 60) covalent geometry : bond 0.00677 (16731) covalent geometry : angle 0.78272 (22722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5109.74 seconds wall clock time: 90 minutes 41.47 seconds (5441.47 seconds total)