Starting phenix.real_space_refine on Sat Oct 11 17:22:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tr3_41569/10_2025/8tr3_41569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tr3_41569/10_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_41569/10_2025/8tr3_41569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tr3_41569/10_2025/8tr3_41569.map" model { file = "/net/cci-nas-00/data/ceres_data/8tr3_41569/10_2025/8tr3_41569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tr3_41569/10_2025/8tr3_41569.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.69, per 1000 atoms: 0.22 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: 1.40 Conformation dependent library (CDL) restraints added in 660.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.73 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: 2.55 Time building geometry restraints manager: 1.88 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: 4.290 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.520 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- 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 : 11.84 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG D 644 TYR 0.008 0.001 TYR C 40 PHE 0.013 0.001 PHE J 29 TRP 0.043 0.002 TRP E 45 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00466 (16731) covalent geometry : angle 0.71973 (22722) SS BOND : bond 0.00614 ( 30) SS BOND : angle 1.51041 ( 60) hydrogen bonds : bond 0.10642 ( 612) hydrogen bonds : angle 5.78374 ( 1647) link_BETA1-4 : bond 0.00597 ( 6) link_BETA1-4 : angle 1.56798 ( 18) link_NAG-ASN : bond 0.00263 ( 33) link_NAG-ASN : angle 1.67611 ( 99) *********************** 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 : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.5568 (tm-30) outliers start: 6 outliers final: 3 residues processed: 263 average time/residue: 0.1702 time to fit residues: 63.1397 Evaluate side-chains 235 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 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 463 ASN D 577 GLN I 97 HIS ** 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 463 ASN F 577 GLN J 97 HIS ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095584 restraints weight = 37150.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095137 restraints weight = 28299.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096308 restraints weight = 23498.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096733 restraints weight = 18880.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096882 restraints weight = 18512.537| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16800 Z= 0.169 Angle : 0.656 7.081 22899 Z= 0.336 Chirality : 0.045 0.190 2682 Planarity : 0.004 0.047 2820 Dihedral : 6.749 49.510 2973 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.38 % Allowed : 23.15 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1968 helix: 1.65 (0.27), residues: 396 sheet: -0.25 (0.20), residues: 678 loop : -2.23 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 82A TYR 0.016 0.001 TYR I 59 PHE 0.014 0.002 PHE E 376 TRP 0.012 0.002 TRP J 36 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00407 (16731) covalent geometry : angle 0.64564 (22722) SS BOND : bond 0.00703 ( 30) SS BOND : angle 1.43054 ( 60) hydrogen bonds : bond 0.04205 ( 612) hydrogen bonds : angle 5.22002 ( 1647) link_BETA1-4 : bond 0.00318 ( 6) link_BETA1-4 : angle 0.96860 ( 18) link_NAG-ASN : bond 0.00279 ( 33) link_NAG-ASN : angle 1.60492 ( 99) *********************** 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 304 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 587 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8947 (mt) REVERT: H 80 MET cc_start: 0.7211 (tpt) cc_final: 0.7002 (tpt) REVERT: L 105 GLU cc_start: 0.6807 (mp0) cc_final: 0.5521 (tm-30) REVERT: D 587 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8935 (mt) REVERT: I 46 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7369 (mt-10) REVERT: M 105 GLU cc_start: 0.6892 (mp0) cc_final: 0.6611 (tm-30) REVERT: E 398 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6869 (p0) REVERT: F 522 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7702 (t80) REVERT: J 38 ARG cc_start: 0.8334 (ptt180) cc_final: 0.8092 (ptt90) REVERT: J 46 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7530 (mt-10) outliers start: 42 outliers final: 22 residues processed: 285 average time/residue: 0.1550 time to fit residues: 63.5069 Evaluate side-chains 254 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 373 THR 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 H residue 82 ARG 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 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN 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 95 MET 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 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 45 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 442 GLN ** H 1 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** C 442 GLN I 39 GLN 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** E 442 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.126598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089645 restraints weight = 37977.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089271 restraints weight = 27652.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090057 restraints weight = 24428.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090331 restraints weight = 20682.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090383 restraints weight = 20149.167| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 16800 Z= 0.323 Angle : 0.803 8.963 22899 Z= 0.407 Chirality : 0.050 0.211 2682 Planarity : 0.004 0.039 2820 Dihedral : 6.807 46.278 2967 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 4.92 % Allowed : 23.66 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.19), residues: 1968 helix: 1.12 (0.26), residues: 402 sheet: -0.30 (0.20), residues: 651 loop : -2.44 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 66 TYR 0.020 0.002 TYR C 486 PHE 0.016 0.002 PHE M 98 TRP 0.018 0.003 TRP B 610 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00770 (16731) covalent geometry : angle 0.78958 (22722) SS BOND : bond 0.00988 ( 30) SS BOND : angle 1.59366 ( 60) hydrogen bonds : bond 0.05076 ( 612) hydrogen bonds : angle 5.39681 ( 1647) link_BETA1-4 : bond 0.00230 ( 6) link_BETA1-4 : angle 0.93851 ( 18) link_NAG-ASN : bond 0.00712 ( 33) link_NAG-ASN : angle 2.04791 ( 99) *********************** 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 338 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 251 time to evaluate : 0.814 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: 0.8504 (OUTLIER) cc_final: 0.7639 (m100) REVERT: B 530 MET cc_start: 0.7649 (mtt) cc_final: 0.7361 (mtt) REVERT: H 46 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7462 (mt-10) REVERT: L 105 GLU cc_start: 0.6992 (mp0) cc_final: 0.6716 (tm-30) REVERT: C 398 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6898 (p0) REVERT: C 479 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.6594 (m100) REVERT: D 587 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8958 (mm) REVERT: I 46 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7483 (mt-10) REVERT: E 479 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.6659 (m100) REVERT: F 522 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8057 (t80) REVERT: J 46 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7619 (mt-10) outliers start: 87 outliers final: 55 residues processed: 315 average time/residue: 0.1451 time to fit residues: 67.2909 Evaluate side-chains 299 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 238 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 244 THR 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 419 ARG 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 520 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 104 LEU 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 236 THR 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 398 ASN 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 587 LEU Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain M residue 90 GLN 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 236 THR Chi-restraints excluded: chain E residue 244 THR 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 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 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 82 ARG Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 142 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 39 optimal weight: 0.0070 chunk 83 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.130546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092924 restraints weight = 37095.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093347 restraints weight = 24380.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094150 restraints weight = 20882.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094690 restraints weight = 18619.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094774 restraints weight = 17689.350| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16800 Z= 0.124 Angle : 0.642 8.327 22899 Z= 0.327 Chirality : 0.045 0.218 2682 Planarity : 0.004 0.045 2820 Dihedral : 5.822 36.189 2967 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.00 % Allowed : 26.71 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.19), residues: 1968 helix: 1.39 (0.27), residues: 417 sheet: -0.19 (0.20), residues: 654 loop : -2.24 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 82A TYR 0.014 0.001 TYR I 59 PHE 0.015 0.002 PHE E 376 TRP 0.013 0.001 TRP C 112 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (16731) covalent geometry : angle 0.63093 (22722) SS BOND : bond 0.00638 ( 30) SS BOND : angle 1.28332 ( 60) hydrogen bonds : bond 0.03729 ( 612) hydrogen bonds : angle 5.10512 ( 1647) link_BETA1-4 : bond 0.00336 ( 6) link_BETA1-4 : angle 0.87408 ( 18) link_NAG-ASN : bond 0.00337 ( 33) link_NAG-ASN : angle 1.72226 ( 99) *********************** 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 314 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 261 time to evaluate : 0.634 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: 0.9194 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: A 479 TRP cc_start: 0.8288 (OUTLIER) cc_final: 0.7172 (m100) REVERT: H 38 ARG cc_start: 0.8411 (ptm160) cc_final: 0.8152 (ptm-80) REVERT: H 46 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7239 (mt-10) REVERT: H 80 MET cc_start: 0.7379 (tpt) cc_final: 0.6994 (tpt) REVERT: L 103 LYS cc_start: 0.8550 (tptp) cc_final: 0.8093 (tptp) REVERT: C 103 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: C 479 TRP cc_start: 0.8159 (OUTLIER) cc_final: 0.6545 (m100) REVERT: I 46 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7384 (mt-10) REVERT: I 66 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8211 (ptm160) REVERT: E 389 ASP cc_start: 0.8806 (t70) cc_final: 0.8391 (p0) REVERT: E 390 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8075 (pp) REVERT: E 479 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.6618 (m100) REVERT: F 522 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8161 (t80) REVERT: J 38 ARG cc_start: 0.8370 (ptt90) cc_final: 0.7968 (ptm-80) REVERT: J 46 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7422 (mt-10) REVERT: J 48 MET cc_start: 0.8389 (mmm) cc_final: 0.8069 (mmm) REVERT: N 78 LEU cc_start: 0.8362 (mt) cc_final: 0.7962 (mt) outliers start: 53 outliers final: 23 residues processed: 298 average time/residue: 0.1466 time to fit residues: 63.5790 Evaluate side-chains 262 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 GLN 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 479 TRP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.090966 restraints weight = 37287.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091230 restraints weight = 25047.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092027 restraints weight = 21722.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092395 restraints weight = 19354.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092423 restraints weight = 19053.378| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1999 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= 0.197 Angle : 0.689 8.766 22899 Z= 0.348 Chirality : 0.046 0.204 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.715 36.065 2967 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.15 % Allowed : 24.56 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 1968 helix: 1.56 (0.27), residues: 399 sheet: -0.14 (0.20), residues: 651 loop : -2.37 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 82A TYR 0.021 0.001 TYR J 59 PHE 0.016 0.002 PHE N 62 TRP 0.021 0.002 TRP I 36 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00475 (16731) covalent geometry : angle 0.67830 (22722) SS BOND : bond 0.00769 ( 30) SS BOND : angle 1.41899 ( 60) hydrogen bonds : bond 0.04074 ( 612) hydrogen bonds : angle 5.06068 ( 1647) link_BETA1-4 : bond 0.00247 ( 6) link_BETA1-4 : angle 0.89690 ( 18) link_NAG-ASN : bond 0.00395 ( 33) link_NAG-ASN : angle 1.63802 ( 99) *********************** 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 335 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 244 time to evaluate : 0.651 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: 0.9292 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: A 479 TRP cc_start: 0.8343 (OUTLIER) cc_final: 0.7232 (m100) REVERT: B 550 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.4582 (pp30) REVERT: H 38 ARG cc_start: 0.8453 (ptm160) cc_final: 0.8196 (ptm-80) REVERT: H 46 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7237 (mt-10) REVERT: L 62 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: L 105 GLU cc_start: 0.6945 (mp0) cc_final: 0.6578 (tm-30) REVERT: C 103 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: C 389 ASP cc_start: 0.8620 (t0) cc_final: 0.8304 (p0) REVERT: C 479 TRP cc_start: 0.8297 (OUTLIER) cc_final: 0.6593 (m100) REVERT: D 550 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.4526 (pp30) REVERT: I 46 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7219 (mt-10) REVERT: M 78 LEU cc_start: 0.8449 (mt) cc_final: 0.8017 (mt) REVERT: M 105 GLU cc_start: 0.5464 (tm-30) cc_final: 0.5229 (tm-30) REVERT: E 57 ASP cc_start: 0.7807 (m-30) cc_final: 0.7320 (m-30) REVERT: E 103 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8789 (tt0) REVERT: E 398 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6787 (p0) REVERT: E 479 TRP cc_start: 0.8351 (OUTLIER) cc_final: 0.6690 (m100) REVERT: F 522 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8147 (t80) REVERT: F 550 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.4582 (pp30) REVERT: J 46 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7436 (mt-10) REVERT: N 103 LYS cc_start: 0.8434 (tptp) cc_final: 0.7676 (ptmt) outliers start: 91 outliers final: 46 residues processed: 312 average time/residue: 0.1349 time to fit residues: 63.1447 Evaluate side-chains 290 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 608 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 104 LEU 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 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 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 522 PHE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 95 MET 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 398 ASN 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 550 GLN Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 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** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN M 79 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.129444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091577 restraints weight = 37135.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092016 restraints weight = 25183.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092902 restraints weight = 20921.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092919 restraints weight = 19953.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093425 restraints weight = 18574.152| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16800 Z= 0.159 Angle : 0.669 9.140 22899 Z= 0.339 Chirality : 0.046 0.310 2682 Planarity : 0.004 0.045 2820 Dihedral : 5.603 35.582 2967 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.47 % Allowed : 25.35 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.19), residues: 1968 helix: 1.34 (0.27), residues: 417 sheet: -0.30 (0.20), residues: 681 loop : -2.31 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 66 TYR 0.015 0.001 TYR M 87 PHE 0.015 0.002 PHE N 62 TRP 0.030 0.002 TRP C 112 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00382 (16731) covalent geometry : angle 0.65483 (22722) SS BOND : bond 0.00695 ( 30) SS BOND : angle 1.33061 ( 60) hydrogen bonds : bond 0.03827 ( 612) hydrogen bonds : angle 4.97506 ( 1647) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 0.90444 ( 18) link_NAG-ASN : bond 0.00264 ( 33) link_NAG-ASN : angle 2.00359 ( 99) *********************** 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: 79 poor density : 244 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: A 479 TRP cc_start: 0.8292 (OUTLIER) cc_final: 0.7126 (m100) REVERT: B 530 MET cc_start: 0.7768 (mtt) cc_final: 0.7311 (mtt) REVERT: B 550 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.4553 (pp30) REVERT: H 46 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7229 (mt-10) REVERT: H 48 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8134 (mtm) REVERT: L 62 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: L 103 LYS cc_start: 0.8382 (tptp) cc_final: 0.8002 (tptp) REVERT: C 103 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: C 389 ASP cc_start: 0.8610 (t0) cc_final: 0.8281 (p0) REVERT: C 479 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.6611 (m100) REVERT: D 550 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.4515 (pp30) REVERT: I 46 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7091 (mt-10) REVERT: M 78 LEU cc_start: 0.8360 (mt) cc_final: 0.8098 (mt) REVERT: M 87 TYR cc_start: 0.7505 (m-80) cc_final: 0.7256 (m-10) REVERT: M 103 LYS cc_start: 0.8344 (tptp) cc_final: 0.7659 (ptmt) REVERT: M 105 GLU cc_start: 0.5743 (tm-30) cc_final: 0.5237 (mp0) REVERT: E 57 ASP cc_start: 0.7860 (m-30) cc_final: 0.7388 (m-30) REVERT: E 103 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8890 (tt0) REVERT: E 389 ASP cc_start: 0.8809 (t70) cc_final: 0.8395 (p0) REVERT: E 479 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.6711 (m100) REVERT: F 522 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8173 (t80) REVERT: F 550 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.4659 (pp30) REVERT: J 38 ARG cc_start: 0.8218 (ptm-80) cc_final: 0.7919 (ptm-80) REVERT: J 46 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7357 (mt-10) REVERT: N 105 GLU cc_start: 0.6416 (mp0) cc_final: 0.4928 (tm-30) outliers start: 79 outliers final: 52 residues processed: 300 average time/residue: 0.1338 time to fit residues: 60.1436 Evaluate side-chains 290 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 67 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 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 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 95 MET Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.127622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098340 restraints weight = 36967.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097652 restraints weight = 35192.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098583 restraints weight = 35044.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099114 restraints weight = 22884.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100260 restraints weight = 20966.160| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2326 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= 0.226 Angle : 0.718 10.337 22899 Z= 0.363 Chirality : 0.047 0.233 2682 Planarity : 0.004 0.045 2820 Dihedral : 5.766 37.725 2967 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 4.98 % Allowed : 25.24 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.19), residues: 1968 helix: 1.46 (0.27), residues: 399 sheet: -0.27 (0.20), residues: 660 loop : -2.44 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 82A TYR 0.014 0.002 TYR N 87 PHE 0.014 0.002 PHE N 62 TRP 0.022 0.002 TRP H 36 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00543 (16731) covalent geometry : angle 0.70701 (22722) SS BOND : bond 0.00791 ( 30) SS BOND : angle 1.41117 ( 60) hydrogen bonds : bond 0.04249 ( 612) hydrogen bonds : angle 5.03412 ( 1647) link_BETA1-4 : bond 0.00257 ( 6) link_BETA1-4 : angle 0.92715 ( 18) link_NAG-ASN : bond 0.00439 ( 33) link_NAG-ASN : angle 1.81398 ( 99) *********************** 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 331 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 246 GLN cc_start: 0.8291 (tp40) cc_final: 0.7898 (tp40) REVERT: A 389 ASP cc_start: 0.8569 (t70) cc_final: 0.8307 (p0) REVERT: A 479 TRP cc_start: 0.8395 (OUTLIER) cc_final: 0.7373 (m100) REVERT: B 550 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.4546 (pp30) REVERT: H 46 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7355 (mt-10) REVERT: L 62 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: L 103 LYS cc_start: 0.8380 (tptp) cc_final: 0.7923 (tptp) REVERT: C 103 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: C 389 ASP cc_start: 0.8463 (t0) cc_final: 0.8255 (p0) REVERT: C 479 TRP cc_start: 0.8371 (OUTLIER) cc_final: 0.6716 (m100) REVERT: D 550 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.4504 (pp30) REVERT: I 46 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7117 (mt-10) REVERT: I 50 TRP cc_start: 0.8225 (p90) cc_final: 0.7932 (p-90) REVERT: E 57 ASP cc_start: 0.7708 (m-30) cc_final: 0.7359 (m-30) REVERT: E 103 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: E 479 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.6789 (m100) REVERT: F 522 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7963 (t80) REVERT: F 550 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.4691 (pp30) REVERT: J 46 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7348 (mt-10) REVERT: N 78 LEU cc_start: 0.8362 (mt) cc_final: 0.8079 (mm) outliers start: 88 outliers final: 62 residues processed: 307 average time/residue: 0.1272 time to fit residues: 59.0088 Evaluate side-chains 307 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 234 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 566 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 593 LEU 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 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 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain N residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 67 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 12 optimal weight: 0.0980 chunk 196 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 47 optimal weight: 8.9990 chunk 181 optimal weight: 0.0370 overall best weight: 0.4460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 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 = 0.3993 r_free = 0.3993 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.101977 restraints weight = 36962.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100893 restraints weight = 30774.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101525 restraints weight = 34766.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102254 restraints weight = 22146.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.102961 restraints weight = 19776.330| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16800 Z= 0.119 Angle : 0.658 9.867 22899 Z= 0.333 Chirality : 0.045 0.213 2682 Planarity : 0.004 0.046 2820 Dihedral : 5.177 34.794 2967 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.17 % Allowed : 27.11 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.19), residues: 1968 helix: 1.43 (0.27), residues: 417 sheet: -0.26 (0.20), residues: 663 loop : -2.27 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.018 0.001 TYR M 87 PHE 0.018 0.002 PHE N 62 TRP 0.022 0.002 TRP A 45 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00280 (16731) covalent geometry : angle 0.64953 (22722) SS BOND : bond 0.00591 ( 30) SS BOND : angle 1.21347 ( 60) hydrogen bonds : bond 0.03443 ( 612) hydrogen bonds : angle 4.88068 ( 1647) link_BETA1-4 : bond 0.00367 ( 6) link_BETA1-4 : angle 0.94214 ( 18) link_NAG-ASN : bond 0.00243 ( 33) link_NAG-ASN : angle 1.47007 ( 99) *********************** 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 308 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: B 530 MET cc_start: 0.7848 (mtt) cc_final: 0.7433 (mtt) REVERT: B 550 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.4668 (pp30) REVERT: H 46 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7208 (mt-10) REVERT: H 59 TYR cc_start: 0.7684 (m-10) cc_final: 0.7448 (m-10) REVERT: H 82 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7612 (mtm-85) REVERT: H 103 TRP cc_start: 0.7974 (m-10) cc_final: 0.7566 (m-10) REVERT: L 78 LEU cc_start: 0.8357 (mt) cc_final: 0.7908 (mt) REVERT: L 103 LYS cc_start: 0.8400 (tptp) cc_final: 0.7909 (tptp) REVERT: C 103 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: C 479 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.6691 (m100) REVERT: D 550 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.4589 (pp30) REVERT: M 78 LEU cc_start: 0.8322 (mt) cc_final: 0.7939 (mt) REVERT: M 103 LYS cc_start: 0.8147 (tptp) cc_final: 0.7476 (ptmt) REVERT: E 57 ASP cc_start: 0.7781 (m-30) cc_final: 0.7490 (m-30) REVERT: E 103 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8806 (tt0) REVERT: E 389 ASP cc_start: 0.8722 (t70) cc_final: 0.8367 (p0) REVERT: F 522 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7895 (t80) REVERT: F 550 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.4749 (pp30) REVERT: J 46 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7208 (mt-10) REVERT: J 103 TRP cc_start: 0.7920 (m-10) cc_final: 0.7438 (m-10) REVERT: N 105 GLU cc_start: 0.6325 (mp0) cc_final: 0.4471 (tm-30) outliers start: 56 outliers final: 41 residues processed: 293 average time/residue: 0.1333 time to fit residues: 58.5391 Evaluate side-chains 279 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 375 SER 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 1 GLN Chi-restraints excluded: chain H residue 11 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 103 GLN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 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 F residue 522 PHE 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 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 109 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 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 = 0.3966 r_free = 0.3966 target = 0.129579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100254 restraints weight = 36873.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.100260 restraints weight = 33428.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100414 restraints weight = 37132.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.101541 restraints weight = 22475.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102274 restraints weight = 19376.212| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16800 Z= 0.170 Angle : 0.689 9.923 22899 Z= 0.348 Chirality : 0.046 0.208 2682 Planarity : 0.004 0.046 2820 Dihedral : 5.232 33.901 2967 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.51 % Allowed : 27.33 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.19), residues: 1968 helix: 1.32 (0.27), residues: 417 sheet: -0.26 (0.20), residues: 660 loop : -2.34 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 83 TYR 0.023 0.001 TYR N 92 PHE 0.018 0.002 PHE N 62 TRP 0.040 0.002 TRP E 112 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00410 (16731) covalent geometry : angle 0.68042 (22722) SS BOND : bond 0.00684 ( 30) SS BOND : angle 1.33698 ( 60) hydrogen bonds : bond 0.03734 ( 612) hydrogen bonds : angle 4.88071 ( 1647) link_BETA1-4 : bond 0.00256 ( 6) link_BETA1-4 : angle 0.93224 ( 18) link_NAG-ASN : bond 0.00293 ( 33) link_NAG-ASN : angle 1.56862 ( 99) *********************** 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 294 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 0.702 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: 0.9190 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: B 530 MET cc_start: 0.7949 (mtt) cc_final: 0.7539 (mtt) REVERT: B 550 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.4683 (pp30) REVERT: H 46 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7188 (mt-10) REVERT: H 59 TYR cc_start: 0.7626 (m-10) cc_final: 0.7407 (m-10) REVERT: H 66 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8236 (ptt-90) REVERT: H 82 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7511 (mtm-85) REVERT: L 103 LYS cc_start: 0.8394 (tptp) cc_final: 0.7867 (tptp) REVERT: C 103 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: C 479 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.6649 (m100) REVERT: D 550 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.4625 (pp30) REVERT: M 78 LEU cc_start: 0.8264 (mt) cc_final: 0.7888 (mt) REVERT: M 105 GLU cc_start: 0.6046 (mp0) cc_final: 0.4835 (tm-30) REVERT: E 57 ASP cc_start: 0.7655 (m-30) cc_final: 0.7330 (m-30) REVERT: E 103 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8897 (tt0) REVERT: E 389 ASP cc_start: 0.8646 (t70) cc_final: 0.8344 (p0) REVERT: E 479 TRP cc_start: 0.8268 (OUTLIER) cc_final: 0.6738 (m100) REVERT: F 522 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7925 (t80) REVERT: F 550 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.4717 (pp30) outliers start: 62 outliers final: 46 residues processed: 278 average time/residue: 0.1355 time to fit residues: 56.5803 Evaluate side-chains 277 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain H residue 11 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 103 GLN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 62 PHE 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 376 PHE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain N residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 151 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 122 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102036 restraints weight = 37052.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100936 restraints weight = 30793.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101459 restraints weight = 35007.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102449 restraints weight = 22204.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103336 restraints weight = 19566.239| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16800 Z= 0.125 Angle : 0.679 12.773 22899 Z= 0.342 Chirality : 0.045 0.356 2682 Planarity : 0.004 0.047 2820 Dihedral : 5.045 32.230 2967 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.23 % Allowed : 27.96 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 1968 helix: 1.41 (0.27), residues: 417 sheet: -0.23 (0.20), residues: 660 loop : -2.30 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 83 TYR 0.019 0.001 TYR N 87 PHE 0.017 0.002 PHE N 62 TRP 0.046 0.002 TRP A 112 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00302 (16731) covalent geometry : angle 0.66720 (22722) SS BOND : bond 0.00590 ( 30) SS BOND : angle 1.22516 ( 60) hydrogen bonds : bond 0.03420 ( 612) hydrogen bonds : angle 4.82640 ( 1647) link_BETA1-4 : bond 0.00324 ( 6) link_BETA1-4 : angle 0.95576 ( 18) link_NAG-ASN : bond 0.00254 ( 33) link_NAG-ASN : angle 1.85479 ( 99) ********************** 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 283 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: B 530 MET cc_start: 0.7924 (mtt) cc_final: 0.7527 (mtt) REVERT: B 550 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.4689 (pp30) REVERT: H 46 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7107 (mt-10) REVERT: H 59 TYR cc_start: 0.7664 (m-10) cc_final: 0.7439 (m-10) REVERT: H 82 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7593 (mtm-85) REVERT: L 105 GLU cc_start: 0.6957 (mp0) cc_final: 0.6494 (tm-30) REVERT: C 103 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: C 479 TRP cc_start: 0.8128 (OUTLIER) cc_final: 0.6673 (m100) REVERT: D 550 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.4687 (pp30) REVERT: M 78 LEU cc_start: 0.8220 (mt) cc_final: 0.7881 (mt) REVERT: M 105 GLU cc_start: 0.6005 (mp0) cc_final: 0.4846 (tm-30) REVERT: E 57 ASP cc_start: 0.7766 (m-30) cc_final: 0.7490 (m-30) REVERT: E 103 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: E 389 ASP cc_start: 0.8659 (t70) cc_final: 0.8354 (p0) REVERT: F 522 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7912 (t80) REVERT: F 550 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.4758 (pp30) REVERT: N 18 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.8013 (ttp80) outliers start: 57 outliers final: 43 residues processed: 271 average time/residue: 0.1370 time to fit residues: 55.8049 Evaluate side-chains 272 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 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 103 GLN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 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 F residue 522 PHE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 38 optimal weight: 0.0770 chunk 49 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 79 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 = 0.3986 r_free = 0.3986 target = 0.130903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.101807 restraints weight = 36866.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101162 restraints weight = 32413.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101482 restraints weight = 35263.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102480 restraints weight = 22234.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.103128 restraints weight = 19363.013| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16800 Z= 0.140 Angle : 0.688 12.631 22899 Z= 0.345 Chirality : 0.045 0.308 2682 Planarity : 0.004 0.066 2820 Dihedral : 5.029 30.721 2967 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.34 % Allowed : 27.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.19), residues: 1968 helix: 1.41 (0.27), residues: 417 sheet: -0.22 (0.20), residues: 660 loop : -2.36 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 83 TYR 0.018 0.001 TYR N 92 PHE 0.017 0.002 PHE N 62 TRP 0.050 0.002 TRP J 103 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00340 (16731) covalent geometry : angle 0.67205 (22722) SS BOND : bond 0.00613 ( 30) SS BOND : angle 1.27010 ( 60) hydrogen bonds : bond 0.03499 ( 612) hydrogen bonds : angle 4.80508 ( 1647) link_BETA1-4 : bond 0.00283 ( 6) link_BETA1-4 : angle 0.95897 ( 18) link_NAG-ASN : bond 0.00283 ( 33) link_NAG-ASN : angle 2.12754 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.51 seconds wall clock time: 50 minutes 30.35 seconds (3030.35 seconds total)