Starting phenix.real_space_refine on Sat Jun 14 16:48:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tr3_41569/06_2025/8tr3_41569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tr3_41569/06_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_41569/06_2025/8tr3_41569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tr3_41569/06_2025/8tr3_41569.map" model { file = "/net/cci-nas-00/data/ceres_data/8tr3_41569/06_2025/8tr3_41569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tr3_41569/06_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-5710/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: 10.55, per 1000 atoms: 0.64 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: 3.98 Conformation dependent library (CDL) restraints added in 1.9 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: 2.00 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: 5.17 Time building geometry restraints manager: 4.75 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: 0.05 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.800 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.040 ------------------------------------------------------------------------------- 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 : 1.683 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: 0.3356 time to fit residues: 124.6483 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 : 1.730 ------------------------------------------------------------------------------- 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 = 0.092638 restraints weight = 37113.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092536 restraints weight = 27808.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093498 restraints weight = 23111.677| |-----------------------------------------------------------------------------| 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 49.793 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 0.89820 ( 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 : 1.777 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: 0.7013 (mtt) REVERT: H 38 ARG cc_start: 0.8390 (ptt180) cc_final: 0.8049 (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: 0.7090 (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: 0.7398 (mt-10) REVERT: M 103 LYS cc_start: 0.8561 (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: 0.8226 (OUTLIER) cc_final: 0.7801 (t80) REVERT: J 38 ARG cc_start: 0.8399 (ptt180) cc_final: 0.8147 (ptt90) REVERT: J 46 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7567 (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: 0.3124 time to fit residues: 134.1510 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 : 1.740 ------------------------------------------------------------------------------- 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: 9.9990 chunk 176 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.130885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101478 restraints weight = 36823.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101485 restraints weight = 33468.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101913 restraints weight = 35452.488| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16800 Z= 0.132 Angle : 0.636 8.777 22899 Z= 0.324 Chirality : 0.045 0.213 2682 Planarity : 0.003 0.041 2820 Dihedral : 6.158 42.842 2967 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.66 % Allowed : 25.35 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1968 helix: 1.69 (0.27), residues: 399 sheet: -0.26 (0.20), residues: 678 loop : -2.25 (0.20), residues: 891 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 0.002 PHE E 376 TYR 0.016 0.001 TYR I 59 ARG 0.004 0.000 ARG J 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 33) link_NAG-ASN : angle 1.65181 ( 99) link_BETA1-4 : bond 0.00371 ( 6) link_BETA1-4 : angle 0.90057 ( 18) hydrogen bonds : bond 0.03887 ( 612) hydrogen bonds : angle 5.13855 ( 1647) SS BOND : bond 0.00665 ( 30) SS BOND : angle 1.32625 ( 60) covalent geometry : bond 0.00312 (16731) covalent geometry : angle 0.62505 (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 302 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 1.784 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: B 530 MET cc_start: 0.7694 (mtt) cc_final: 0.7227 (mtt) REVERT: H 46 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7388 (mt-10) REVERT: L 103 LYS cc_start: 0.8137 (tptp) cc_final: 0.7686 (tptp) REVERT: C 114 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8161 (tm-30) REVERT: I 46 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7341 (mt-10) REVERT: M 105 GLU cc_start: 0.6459 (mp0) cc_final: 0.6196 (tm-30) REVERT: E 398 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.6956 (p0) REVERT: F 522 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7733 (t80) REVERT: J 46 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7494 (mt-10) REVERT: N 103 LYS cc_start: 0.8144 (tptp) cc_final: 0.7866 (tptp) outliers start: 47 outliers final: 32 residues processed: 285 average time/residue: 0.3068 time to fit residues: 126.8644 Evaluate side-chains 266 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 376 PHE 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 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: 8.9990 chunk 73 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 155 optimal weight: 0.0020 chunk 168 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- 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 39 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** J 39 GLN N 38 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.129856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.091903 restraints weight = 37115.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092566 restraints weight = 25025.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093497 restraints weight = 20943.046| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16800 Z= 0.174 Angle : 0.656 7.944 22899 Z= 0.333 Chirality : 0.046 0.227 2682 Planarity : 0.004 0.043 2820 Dihedral : 5.824 35.210 2967 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.24 % Allowed : 25.07 % Favored : 70.68 % 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: 1.35 (0.27), residues: 417 sheet: -0.14 (0.20), residues: 651 loop : -2.23 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 100F HIS 0.004 0.001 HIS E 374 PHE 0.015 0.002 PHE E 376 TYR 0.014 0.001 TYR I 59 ARG 0.007 0.001 ARG J 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 33) link_NAG-ASN : angle 1.77114 ( 99) link_BETA1-4 : bond 0.00352 ( 6) link_BETA1-4 : angle 0.88707 ( 18) hydrogen bonds : bond 0.03972 ( 612) hydrogen bonds : angle 5.07186 ( 1647) SS BOND : bond 0.00726 ( 30) SS BOND : angle 1.37921 ( 60) covalent geometry : bond 0.00418 (16731) covalent geometry : angle 0.64395 (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 332 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 257 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7277 (m100) REVERT: H 46 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7228 (mt-10) REVERT: H 48 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: H 82 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7363 (mtm-85) REVERT: L 103 LYS cc_start: 0.8407 (tptp) cc_final: 0.7899 (tptp) REVERT: C 479 TRP cc_start: 0.8272 (OUTLIER) cc_final: 0.6431 (m100) REVERT: I 46 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7302 (mt-10) REVERT: M 14 SER cc_start: 0.9044 (m) cc_final: 0.8804 (p) REVERT: M 78 LEU cc_start: 0.8344 (mt) cc_final: 0.8128 (mt) REVERT: M 103 LYS cc_start: 0.8229 (tptp) cc_final: 0.7768 (tptp) REVERT: E 398 ASN cc_start: 0.7310 (OUTLIER) cc_final: 0.6929 (p0) REVERT: E 479 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.6620 (m100) REVERT: F 522 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8122 (t80) REVERT: J 46 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7425 (mt-10) REVERT: N 105 GLU cc_start: 0.7253 (mp0) cc_final: 0.6990 (tm-30) outliers start: 75 outliers final: 42 residues processed: 312 average time/residue: 0.2876 time to fit residues: 131.1580 Evaluate side-chains 280 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 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 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 287 HIS 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 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR 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 593 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 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 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 593 LEU Chi-restraints excluded: chain F residue 598 CYS 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: 1.9990 chunk 52 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 178 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- 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 39 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** J 39 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.128800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090475 restraints weight = 37431.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091049 restraints weight = 24770.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092124 restraints weight = 20646.718| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16800 Z= 0.206 Angle : 0.684 8.939 22899 Z= 0.347 Chirality : 0.046 0.262 2682 Planarity : 0.004 0.042 2820 Dihedral : 5.769 36.034 2967 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.04 % Allowed : 24.62 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1968 helix: 1.54 (0.27), residues: 399 sheet: -0.18 (0.20), residues: 651 loop : -2.31 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 338 HIS 0.005 0.001 HIS A 287 PHE 0.015 0.002 PHE E 376 TYR 0.012 0.001 TYR H 59 ARG 0.007 0.001 ARG I 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 33) link_NAG-ASN : angle 1.68724 ( 99) link_BETA1-4 : bond 0.00294 ( 6) link_BETA1-4 : angle 0.88832 ( 18) hydrogen bonds : bond 0.04125 ( 612) hydrogen bonds : angle 5.07902 ( 1647) SS BOND : bond 0.00777 ( 30) SS BOND : angle 1.40634 ( 60) covalent geometry : bond 0.00495 (16731) covalent geometry : angle 0.67361 (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 331 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 242 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: A 479 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7431 (m100) REVERT: B 530 MET cc_start: 0.7666 (mtt) cc_final: 0.7209 (mtt) REVERT: B 550 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.4624 (pp30) REVERT: H 46 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7195 (mt-10) REVERT: H 82 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: L 62 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: L 79 GLN cc_start: 0.7646 (mp-120) cc_final: 0.7356 (mp-120) REVERT: L 105 GLU cc_start: 0.7099 (mp0) cc_final: 0.6798 (tm-30) REVERT: C 103 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: C 479 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.6509 (m100) REVERT: D 550 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.4566 (pp30) REVERT: I 46 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7227 (mt-10) REVERT: M 105 GLU cc_start: 0.6739 (mp0) cc_final: 0.6074 (tm-30) REVERT: E 103 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: E 389 ASP cc_start: 0.8841 (t70) cc_final: 0.8426 (p0) REVERT: E 479 TRP cc_start: 0.8385 (OUTLIER) cc_final: 0.6694 (m100) REVERT: F 522 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8120 (t80) REVERT: F 550 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.4592 (pp30) REVERT: J 46 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7377 (mt-10) REVERT: N 103 LYS cc_start: 0.8316 (tptp) cc_final: 0.8086 (tptp) outliers start: 89 outliers final: 57 residues processed: 311 average time/residue: 0.2857 time to fit residues: 132.9570 Evaluate side-chains 296 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 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 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL 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 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 593 LEU Chi-restraints excluded: chain D residue 598 CYS 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 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 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 66 ARG Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** 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 = 0.3983 r_free = 0.3983 target = 0.130807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102053 restraints weight = 36967.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101127 restraints weight = 33424.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101831 restraints weight = 35381.674| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1933 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= 0.129 Angle : 0.642 8.269 22899 Z= 0.325 Chirality : 0.045 0.283 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.391 34.589 2967 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.41 % Allowed : 25.92 % Favored : 69.67 % 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: -1.09 (0.19), residues: 1968 helix: 1.44 (0.27), residues: 417 sheet: -0.29 (0.20), residues: 678 loop : -2.21 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 112 HIS 0.003 0.001 HIS E 105 PHE 0.014 0.002 PHE E 376 TYR 0.014 0.001 TYR H 59 ARG 0.007 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 33) link_NAG-ASN : angle 1.80911 ( 99) link_BETA1-4 : bond 0.00332 ( 6) link_BETA1-4 : angle 0.90391 ( 18) hydrogen bonds : bond 0.03604 ( 612) hydrogen bonds : angle 4.94138 ( 1647) SS BOND : bond 0.00627 ( 30) SS BOND : angle 1.27479 ( 60) covalent geometry : bond 0.00306 (16731) covalent geometry : angle 0.62974 (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 323 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 245 time to evaluate : 1.745 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: 0.9152 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: A 479 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7271 (m100) REVERT: B 530 MET cc_start: 0.7759 (mtt) cc_final: 0.7449 (mtt) REVERT: B 550 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.4575 (pp30) REVERT: H 48 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7751 (mtm) REVERT: H 66 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8385 (mtm-85) REVERT: H 82 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7333 (mtm-85) REVERT: L 103 LYS cc_start: 0.8222 (tptp) cc_final: 0.7847 (tptp) REVERT: C 103 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: C 104 MET cc_start: 0.8667 (ttm) cc_final: 0.8036 (ttm) REVERT: C 479 TRP cc_start: 0.8118 (OUTLIER) cc_final: 0.6491 (m100) REVERT: D 550 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.4599 (pp30) REVERT: I 38 ARG cc_start: 0.8189 (ptm-80) cc_final: 0.7913 (ptm-80) REVERT: I 46 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7027 (mt-10) REVERT: I 48 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7471 (mtm) REVERT: M 78 LEU cc_start: 0.8296 (mt) cc_final: 0.8089 (mm) REVERT: M 103 LYS cc_start: 0.7823 (tptp) cc_final: 0.7513 (tptp) REVERT: E 103 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: E 479 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.6698 (m100) REVERT: F 522 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7868 (t80) REVERT: F 550 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.4682 (pp30) REVERT: J 46 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7282 (mt-10) REVERT: N 78 LEU cc_start: 0.8436 (mt) cc_final: 0.7916 (mt) REVERT: N 103 LYS cc_start: 0.8189 (tptp) cc_final: 0.7927 (tptp) outliers start: 78 outliers final: 50 residues processed: 303 average time/residue: 0.2945 time to fit residues: 132.2176 Evaluate side-chains 287 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 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 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 103 GLN Chi-restraints excluded: chain C residue 244 THR 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 522 PHE 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 66 ARG 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 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 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 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: 5.9990 chunk 168 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 88 optimal weight: 0.0370 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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** ** 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 = 0.3969 r_free = 0.3969 target = 0.129746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099253 restraints weight = 36816.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.100234 restraints weight = 35637.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101069 restraints weight = 30345.671| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16800 Z= 0.164 Angle : 0.669 9.196 22899 Z= 0.337 Chirality : 0.045 0.203 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.332 34.009 2967 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.02 % Allowed : 26.94 % Favored : 69.04 % 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: 1.35 (0.27), residues: 417 sheet: -0.29 (0.20), residues: 678 loop : -2.24 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.002 PHE E 376 TYR 0.012 0.001 TYR H 59 ARG 0.008 0.001 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 33) link_NAG-ASN : angle 1.62730 ( 99) link_BETA1-4 : bond 0.00272 ( 6) link_BETA1-4 : angle 0.89270 ( 18) hydrogen bonds : bond 0.03775 ( 612) hydrogen bonds : angle 4.91226 ( 1647) SS BOND : bond 0.00690 ( 30) SS BOND : angle 1.33697 ( 60) covalent geometry : bond 0.00396 (16731) covalent geometry : angle 0.65875 (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 315 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: A 104 MET cc_start: 0.8705 (ttm) cc_final: 0.8357 (ttm) REVERT: A 479 TRP cc_start: 0.8264 (OUTLIER) cc_final: 0.7194 (m100) REVERT: B 550 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.4658 (pp30) REVERT: H 46 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7423 (mt-10) REVERT: H 48 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7610 (mtm) REVERT: H 66 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8176 (ptm160) REVERT: H 82 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7286 (mtm-85) REVERT: L 103 LYS cc_start: 0.8236 (tptp) cc_final: 0.7778 (tptp) REVERT: C 389 ASP cc_start: 0.8517 (t70) cc_final: 0.8282 (p0) REVERT: C 479 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.6496 (m100) REVERT: D 550 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.4646 (pp30) REVERT: I 46 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7012 (mt-10) REVERT: I 48 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7376 (mtm) REVERT: M 103 LYS cc_start: 0.7798 (tptp) cc_final: 0.7401 (tptp) REVERT: E 103 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8899 (tt0) REVERT: E 389 ASP cc_start: 0.8714 (t70) cc_final: 0.8412 (p0) REVERT: E 479 TRP cc_start: 0.8245 (OUTLIER) cc_final: 0.6767 (m100) REVERT: F 522 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7852 (t80) REVERT: F 550 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.4811 (pp30) REVERT: J 46 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7237 (mt-10) REVERT: N 103 LYS cc_start: 0.8214 (tptp) cc_final: 0.7815 (tptp) outliers start: 71 outliers final: 50 residues processed: 291 average time/residue: 0.3003 time to fit residues: 128.2972 Evaluate side-chains 293 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 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 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 608 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 66 ARG 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 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 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 Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 17 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097489 restraints weight = 37351.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098927 restraints weight = 36457.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099525 restraints weight = 28478.110| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16800 Z= 0.239 Angle : 0.735 10.406 22899 Z= 0.371 Chirality : 0.048 0.269 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.736 38.897 2967 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 4.58 % Allowed : 26.37 % Favored : 69.04 % 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: -1.27 (0.19), residues: 1968 helix: 1.46 (0.27), residues: 399 sheet: -0.37 (0.20), residues: 678 loop : -2.36 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 112 HIS 0.005 0.001 HIS C 374 PHE 0.015 0.002 PHE E 376 TYR 0.018 0.002 TYR J 59 ARG 0.008 0.001 ARG J 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 33) link_NAG-ASN : angle 1.99294 ( 99) link_BETA1-4 : bond 0.00205 ( 6) link_BETA1-4 : angle 0.89545 ( 18) hydrogen bonds : bond 0.04300 ( 612) hydrogen bonds : angle 5.06166 ( 1647) SS BOND : bond 0.00804 ( 30) SS BOND : angle 1.41354 ( 60) covalent geometry : bond 0.00574 (16731) covalent geometry : angle 0.72211 (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 320 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 239 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: A 479 TRP cc_start: 0.8426 (OUTLIER) cc_final: 0.7511 (m100) REVERT: B 530 MET cc_start: 0.7770 (mtt) cc_final: 0.7343 (mtt) REVERT: B 550 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.4589 (pp30) REVERT: H 46 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7424 (mt-10) REVERT: H 48 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7708 (mtm) REVERT: H 66 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8175 (ptm160) REVERT: H 82 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7299 (mtm-85) REVERT: L 62 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: L 105 GLU cc_start: 0.7027 (mp0) cc_final: 0.6663 (tm-30) REVERT: C 103 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: C 479 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.6584 (m100) REVERT: D 550 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.4582 (pp30) REVERT: I 46 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7151 (mt-10) REVERT: I 48 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7407 (mtm) REVERT: M 103 LYS cc_start: 0.7802 (tptp) cc_final: 0.7271 (tptp) REVERT: E 103 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: E 479 TRP cc_start: 0.8428 (OUTLIER) cc_final: 0.6773 (m100) REVERT: F 522 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7902 (t80) REVERT: F 550 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.4778 (pp30) REVERT: J 46 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7263 (mt-10) REVERT: N 105 GLU cc_start: 0.7228 (mp0) cc_final: 0.6917 (tm-30) outliers start: 81 outliers final: 59 residues processed: 297 average time/residue: 0.2926 time to fit residues: 128.6218 Evaluate side-chains 304 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 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 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 11 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 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 66 ARG 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 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 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 99 VAL Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 39 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 182 optimal weight: 9.9990 chunk 78 optimal weight: 0.0060 chunk 75 optimal weight: 0.7980 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 79 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.131261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100918 restraints weight = 36978.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101876 restraints weight = 34279.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102293 restraints weight = 29985.678| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16800 Z= 0.128 Angle : 0.669 10.693 22899 Z= 0.338 Chirality : 0.045 0.253 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.237 34.879 2967 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.96 % Allowed : 27.33 % Favored : 68.70 % 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: 1.42 (0.27), residues: 417 sheet: -0.35 (0.20), residues: 678 loop : -2.24 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 112 HIS 0.003 0.001 HIS E 105 PHE 0.017 0.001 PHE N 62 TYR 0.021 0.001 TYR H 59 ARG 0.008 0.001 ARG I 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 33) link_NAG-ASN : angle 1.59653 ( 99) link_BETA1-4 : bond 0.00327 ( 6) link_BETA1-4 : angle 0.92371 ( 18) hydrogen bonds : bond 0.03515 ( 612) hydrogen bonds : angle 4.87215 ( 1647) SS BOND : bond 0.00600 ( 30) SS BOND : angle 1.20767 ( 60) covalent geometry : bond 0.00305 (16731) covalent geometry : angle 0.66011 (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 312 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 242 time to evaluate : 1.739 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: 0.9163 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: A 479 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.7196 (m100) REVERT: B 550 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.4642 (pp30) REVERT: H 46 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7400 (mt-10) REVERT: H 48 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7651 (mtm) REVERT: H 66 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8175 (ptm160) REVERT: H 82 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: C 103 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: C 389 ASP cc_start: 0.8541 (t70) cc_final: 0.8293 (p0) REVERT: C 390 LEU cc_start: 0.8389 (pp) cc_final: 0.8079 (pp) REVERT: C 479 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.6613 (m100) REVERT: D 550 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.4674 (pp30) REVERT: I 46 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6989 (mt-10) REVERT: M 105 GLU cc_start: 0.6551 (mp0) cc_final: 0.5720 (tm-30) REVERT: E 103 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8858 (tt0) REVERT: E 389 ASP cc_start: 0.8723 (t70) cc_final: 0.8421 (p0) REVERT: E 479 TRP cc_start: 0.8136 (OUTLIER) cc_final: 0.6689 (m100) REVERT: F 522 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7941 (t80) REVERT: F 550 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.4715 (pp30) REVERT: N 78 LEU cc_start: 0.8427 (mt) cc_final: 0.7828 (mt) outliers start: 70 outliers final: 53 residues processed: 292 average time/residue: 0.3154 time to fit residues: 138.2095 Evaluate side-chains 293 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 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 D residue 550 GLN Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 66 ARG 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 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 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 71 THR Chi-restraints excluded: chain N residue 104 LEU 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: 0.3980 chunk 124 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 158 optimal weight: 3.9990 chunk 178 optimal weight: 0.0050 chunk 40 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN E 258 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 = 0.4015 r_free = 0.4015 target = 0.132595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.102572 restraints weight = 37284.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103875 restraints weight = 36175.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104870 restraints weight = 26565.484| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16800 Z= 0.123 Angle : 0.665 11.677 22899 Z= 0.334 Chirality : 0.045 0.239 2682 Planarity : 0.004 0.053 2820 Dihedral : 4.949 31.700 2967 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.34 % Allowed : 28.18 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1968 helix: 1.45 (0.27), residues: 417 sheet: -0.35 (0.20), residues: 678 loop : -2.24 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP J 103 HIS 0.002 0.001 HIS E 105 PHE 0.017 0.001 PHE N 62 TYR 0.020 0.001 TYR N 92 ARG 0.009 0.001 ARG I 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 33) link_NAG-ASN : angle 1.53937 ( 99) link_BETA1-4 : bond 0.00462 ( 6) link_BETA1-4 : angle 0.98609 ( 18) hydrogen bonds : bond 0.03354 ( 612) hydrogen bonds : angle 4.81768 ( 1647) SS BOND : bond 0.00576 ( 30) SS BOND : angle 1.23804 ( 60) covalent geometry : bond 0.00296 (16731) covalent geometry : angle 0.65617 (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 297 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: B 530 MET cc_start: 0.7688 (mtt) cc_final: 0.7239 (mtt) REVERT: B 550 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.4722 (pp30) REVERT: H 46 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7310 (mt-10) REVERT: H 48 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: H 66 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8099 (ptm160) REVERT: H 82 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7449 (mtm-85) REVERT: C 103 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: C 389 ASP cc_start: 0.8503 (t70) cc_final: 0.8294 (p0) REVERT: C 390 LEU cc_start: 0.8370 (pp) cc_final: 0.8049 (pp) REVERT: C 479 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.6614 (m100) REVERT: D 550 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.4635 (pp30) REVERT: I 48 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7425 (mtm) REVERT: M 18 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.8018 (ttp80) REVERT: E 103 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8865 (tt0) REVERT: E 389 ASP cc_start: 0.8664 (t70) cc_final: 0.8389 (p0) REVERT: F 522 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7922 (t80) REVERT: F 550 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.4760 (pp30) outliers start: 59 outliers final: 47 residues processed: 280 average time/residue: 0.2818 time to fit residues: 117.2952 Evaluate side-chains 282 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 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 H residue 11 VAL 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 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 522 PHE 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 I residue 48 MET Chi-restraints excluded: chain I residue 66 ARG 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 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 376 PHE Chi-restraints excluded: chain E residue 394 THR 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 608 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain N residue 104 LEU 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: 7.9990 chunk 53 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.130071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099799 restraints weight = 36981.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101258 restraints weight = 35745.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101805 restraints weight = 26647.552| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16800 Z= 0.180 Angle : 0.706 12.457 22899 Z= 0.354 Chirality : 0.046 0.221 2682 Planarity : 0.004 0.056 2820 Dihedral : 5.186 31.889 2967 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.90 % Allowed : 27.62 % Favored : 68.48 % 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: -1.26 (0.19), residues: 1968 helix: 1.33 (0.27), residues: 417 sheet: -0.44 (0.20), residues: 657 loop : -2.26 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 103 HIS 0.004 0.001 HIS C 374 PHE 0.018 0.002 PHE N 62 TYR 0.021 0.001 TYR N 87 ARG 0.008 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 33) link_NAG-ASN : angle 1.63787 ( 99) link_BETA1-4 : bond 0.00257 ( 6) link_BETA1-4 : angle 0.96383 ( 18) hydrogen bonds : bond 0.03832 ( 612) hydrogen bonds : angle 4.87852 ( 1647) SS BOND : bond 0.00696 ( 30) SS BOND : angle 1.33754 ( 60) covalent geometry : bond 0.00436 (16731) covalent geometry : angle 0.69696 (22722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5350.21 seconds wall clock time: 93 minutes 31.04 seconds (5611.04 seconds total)