Starting phenix.real_space_refine on Tue Jun 17 12:16:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb4_40290/06_2025/8sb4_40290_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb4_40290/06_2025/8sb4_40290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sb4_40290/06_2025/8sb4_40290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb4_40290/06_2025/8sb4_40290.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb4_40290/06_2025/8sb4_40290_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb4_40290/06_2025/8sb4_40290_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 135 5.16 5 C 12525 2.51 5 N 3345 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20041 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "I" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "M" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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 Time building chain proxies: 12.61, per 1000 atoms: 0.63 Number of scatterers: 20041 At special positions: 0 Unit cell: (158.834, 159.9, 137.514, 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 135 16.00 O 4036 8.00 N 3345 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 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 C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " 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 ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN U 4 " - " MAN U 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 8 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 5.30 Conformation dependent library (CDL) restraints added in 2.8 seconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4578 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 35 sheets defined 19.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.882A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.157A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.962A pdb=" N ASP A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.562A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.626A pdb=" N TRP B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 611 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.653A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.164A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.753A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 61 removed outlier: 4.488A pdb=" N TYR F 61 " --> pdb=" O ALA F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 61' Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.110A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 334 through 351 removed outlier: 3.973A pdb=" N ASP F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.544A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 535 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 573 through 596 removed outlier: 3.545A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.581A pdb=" N TRP G 614 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 615' Processing helix chain 'G' and resid 618 through 624 removed outlier: 3.658A pdb=" N ILE G 622 " --> pdb=" O ASN G 618 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.756A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 636 " --> pdb=" O ASP G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 4.413A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 657 " --> pdb=" O GLN G 653 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA G 662 " --> pdb=" O GLN G 658 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.728A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 61 removed outlier: 4.413A pdb=" N TYR K 61 " --> pdb=" O ALA K 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 61' Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.813A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.190A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 removed outlier: 3.973A pdb=" N ASP K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN K 343 " --> pdb=" O ASN K 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS K 351 " --> pdb=" O ILE K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 475 through 481 Processing helix chain 'K' and resid 482 through 484 No H-bonds generated for 'chain 'K' and resid 482 through 484' Processing helix chain 'L' and resid 529 through 535 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 573 through 596 removed outlier: 3.536A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 removed outlier: 3.803A pdb=" N TRP L 614 " --> pdb=" O ASN L 611 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER L 615 " --> pdb=" O SER L 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 611 through 615' Processing helix chain 'L' and resid 618 through 624 removed outlier: 3.560A pdb=" N ASP L 624 " --> pdb=" O SER L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.722A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 635 " --> pdb=" O TRP L 631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 636 " --> pdb=" O ASP L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 4.099A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN L 651 " --> pdb=" O GLU L 647 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU L 657 " --> pdb=" O GLN L 653 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 662 " --> pdb=" O GLN L 658 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.794A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.263A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (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 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 176 removed outlier: 6.181A pdb=" N LYS A 168 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A 163 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.622A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.550A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 386 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.551A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 39 removed outlier: 6.599A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 59 current: chain 'C' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.391A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.440A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR G 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.374A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'F' and resid 166 through 176 removed outlier: 6.165A pdb=" N LYS F 168 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR F 163 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.602A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 260 current: chain 'F' and resid 284 through 308 removed outlier: 6.457A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 316 through 323 current: chain 'F' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 386 current: chain 'F' and resid 467 through 470 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.623A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.592A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 20 through 22 Processing sheet with id=AC5, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.506A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.481A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR L 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.204A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'K' and resid 166 through 176 removed outlier: 6.128A pdb=" N LYS K 168 " --> pdb=" O THR K 163 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR K 163 " --> pdb=" O LYS K 168 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS K 170 " --> pdb=" O THR K 161 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.562A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 271 through 273 removed outlier: 6.556A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 316 through 323 current: chain 'K' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 381 through 386 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD4, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.594A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.682A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AD7, first strand: chain 'N' and resid 20 through 23 Processing sheet with id=AD8, first strand: chain 'N' and resid 47 through 50 removed outlier: 6.432A pdb=" N TRP N 37 " --> pdb=" O ILE N 49 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1419 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: 8.60 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6356 1.35 - 1.49: 5447 1.49 - 1.62: 8481 1.62 - 1.76: 0 1.76 - 1.89: 183 Bond restraints: 20467 Sorted by residual: bond pdb=" N VAL N 60 " pdb=" CA VAL N 60 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.37e+00 bond pdb=" C2 MAN R 5 " pdb=" O2 MAN R 5 " ideal model delta sigma weight residual 1.407 1.467 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" C HIS N 41 " pdb=" N PRO N 42 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.62e+00 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.585 -0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" N VAL D 60 " pdb=" CA VAL D 60 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.50e+00 ... (remaining 20462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 26941 2.28 - 4.56: 744 4.56 - 6.84: 128 6.84 - 9.12: 21 9.12 - 11.40: 6 Bond angle restraints: 27840 Sorted by residual: angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.10 -11.40 1.80e+00 3.09e-01 4.01e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.65 -10.95 1.80e+00 3.09e-01 3.70e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.16 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C ASN A 403 " pdb=" N SER A 404 " pdb=" CA SER A 404 " ideal model delta sigma weight residual 121.70 131.95 -10.25 1.80e+00 3.09e-01 3.24e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 131.90 -10.20 1.80e+00 3.09e-01 3.21e+01 ... (remaining 27835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 11970 21.59 - 43.18: 781 43.18 - 64.77: 78 64.77 - 86.36: 83 86.36 - 107.94: 38 Dihedral angle restraints: 12950 sinusoidal: 5786 harmonic: 7164 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -173.13 87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS L 598 " pdb=" SG CYS L 598 " pdb=" SG CYS L 604 " pdb=" CB CYS L 604 " ideal model delta sinusoidal sigma weight residual -86.00 -159.15 73.15 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 12947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2690 0.062 - 0.123: 466 0.123 - 0.184: 115 0.184 - 0.246: 8 0.246 - 0.307: 10 Chirality restraints: 3289 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3286 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 75 " -0.062 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO K 76 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO K 76 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 76 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.018 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP F 112 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 585 " -0.236 9.50e-02 1.11e+02 1.06e-01 7.40e+00 pdb=" NE ARG B 585 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 585 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 585 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 585 " -0.004 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 234 2.64 - 3.20: 18054 3.20 - 3.77: 28572 3.77 - 4.33: 41555 4.33 - 4.90: 68057 Nonbonded interactions: 156472 Sorted by model distance: nonbonded pdb=" OG1 THR D 5 " pdb=" OG1 THR D 23 " model vdw 2.071 3.040 nonbonded pdb=" OG1 THR N 5 " pdb=" OG1 THR N 23 " model vdw 2.073 3.040 nonbonded pdb=" OG1 THR I 5 " pdb=" OG1 THR I 23 " model vdw 2.090 3.040 nonbonded pdb=" O THR M 30 " pdb=" OG SER M 54 " model vdw 2.098 3.040 nonbonded pdb=" OG1 THR F 163 " pdb=" OE1 GLU F 164 " model vdw 2.117 3.040 ... (remaining 156467 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'J' and (resid 2 or resid 5 through 9)) selection = (chain 'R' and (resid 1 or resid 4 through 8)) selection = (chain 'V' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 48.280 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.006 0.084 20565 Z= 0.273 Angle : 0.973 11.405 28092 Z= 0.498 Chirality : 0.054 0.307 3289 Planarity : 0.006 0.106 3480 Dihedral : 16.323 107.944 8246 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.83 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2466 helix: -1.74 (0.24), residues: 354 sheet: -0.26 (0.19), residues: 660 loop : -1.20 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 112 HIS 0.008 0.002 HIS I 41 PHE 0.017 0.002 PHE K 391 TYR 0.020 0.002 TYR D 51 ARG 0.016 0.001 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 12) link_NAG-ASN : angle 2.08267 ( 36) link_ALPHA1-6 : bond 0.01107 ( 6) link_ALPHA1-6 : angle 3.87267 ( 18) link_BETA1-4 : bond 0.00604 ( 21) link_BETA1-4 : angle 3.69812 ( 63) link_ALPHA1-2 : bond 0.01461 ( 11) link_ALPHA1-2 : angle 3.99413 ( 33) link_ALPHA1-3 : bond 0.00922 ( 6) link_ALPHA1-3 : angle 4.06036 ( 18) hydrogen bonds : bond 0.21934 ( 534) hydrogen bonds : angle 8.46713 ( 1419) SS BOND : bond 0.00473 ( 42) SS BOND : angle 1.79668 ( 84) covalent geometry : bond 0.00563 (20467) covalent geometry : angle 0.93279 (27840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6775 (m-30) cc_final: 0.6556 (m-30) REVERT: A 121 LYS cc_start: 0.7017 (ptpt) cc_final: 0.6689 (ttmm) REVERT: B 535 MET cc_start: 0.8113 (mtt) cc_final: 0.7418 (mtt) REVERT: B 632 ASP cc_start: 0.7977 (t70) cc_final: 0.7567 (t0) REVERT: B 661 LEU cc_start: 0.8854 (tp) cc_final: 0.8465 (mt) REVERT: C 7 SER cc_start: 0.7703 (p) cc_final: 0.7294 (p) REVERT: C 21 SER cc_start: 0.7955 (p) cc_final: 0.7623 (t) REVERT: C 43 GLN cc_start: 0.7377 (tp40) cc_final: 0.6783 (mp10) REVERT: C 84 ASN cc_start: 0.8031 (t0) cc_final: 0.7798 (t0) REVERT: D 92 SER cc_start: 0.8913 (p) cc_final: 0.8694 (p) REVERT: F 54 CYS cc_start: 0.5359 (p) cc_final: 0.5133 (p) REVERT: F 103 GLN cc_start: 0.7654 (mt0) cc_final: 0.7146 (tm-30) REVERT: F 442 ASN cc_start: 0.8083 (p0) cc_final: 0.7867 (p0) REVERT: G 604 CYS cc_start: 0.6761 (t) cc_final: 0.6492 (t) REVERT: G 632 ASP cc_start: 0.7831 (t70) cc_final: 0.7434 (t0) REVERT: G 660 LEU cc_start: 0.7691 (mt) cc_final: 0.7289 (tt) REVERT: G 661 LEU cc_start: 0.8850 (tp) cc_final: 0.8439 (mt) REVERT: H 13 LYS cc_start: 0.7485 (mmpt) cc_final: 0.7262 (mmtt) REVERT: H 43 GLN cc_start: 0.7495 (tp40) cc_final: 0.6727 (mp10) REVERT: H 84 ASN cc_start: 0.8452 (t0) cc_final: 0.8185 (t0) REVERT: I 25 THR cc_start: 0.8086 (t) cc_final: 0.7589 (m) REVERT: I 36 SER cc_start: 0.8859 (m) cc_final: 0.8656 (t) REVERT: I 38 TYR cc_start: 0.8087 (m-80) cc_final: 0.7114 (m-80) REVERT: I 93 TYR cc_start: 0.8918 (t80) cc_final: 0.8391 (t80) REVERT: K 162 THR cc_start: 0.8345 (m) cc_final: 0.8053 (p) REVERT: L 608 VAL cc_start: 0.8485 (t) cc_final: 0.7955 (t) REVERT: L 634 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7844 (mt-10) REVERT: M 122 LEU cc_start: 0.7846 (mt) cc_final: 0.7435 (mp) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.3238 time to fit residues: 309.1857 Evaluate side-chains 420 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 6 GLN F 287 HIS F 352 HIS G 575 GLN H 43 GLN H 113 ASN K 287 HIS K 352 HIS L 630 GLN L 658 GLN M 6 GLN M 39 GLN M 43 GLN N 41 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120133 restraints weight = 29814.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119825 restraints weight = 23903.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121013 restraints weight = 24483.259| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20565 Z= 0.240 Angle : 0.788 9.746 28092 Z= 0.402 Chirality : 0.050 0.341 3289 Planarity : 0.005 0.060 3480 Dihedral : 12.012 78.575 3794 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.66 % Favored : 94.97 % Rotamer: Outliers : 2.69 % Allowed : 10.49 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.16), residues: 2466 helix: -1.55 (0.25), residues: 375 sheet: -0.24 (0.18), residues: 708 loop : -1.11 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 35 HIS 0.006 0.001 HIS C 35 PHE 0.019 0.003 PHE F 376 TYR 0.025 0.002 TYR D 93 ARG 0.011 0.001 ARG I 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 12) link_NAG-ASN : angle 1.76552 ( 36) link_ALPHA1-6 : bond 0.00704 ( 6) link_ALPHA1-6 : angle 1.88287 ( 18) link_BETA1-4 : bond 0.00506 ( 21) link_BETA1-4 : angle 2.49098 ( 63) link_ALPHA1-2 : bond 0.00700 ( 11) link_ALPHA1-2 : angle 2.28372 ( 33) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 2.10657 ( 18) hydrogen bonds : bond 0.05532 ( 534) hydrogen bonds : angle 6.53130 ( 1419) SS BOND : bond 0.00563 ( 42) SS BOND : angle 1.55823 ( 84) covalent geometry : bond 0.00562 (20467) covalent geometry : angle 0.76800 (27840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 428 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7356 (ptpt) cc_final: 0.7090 (ttmm) REVERT: A 207 LYS cc_start: 0.7306 (tmtt) cc_final: 0.6625 (tmtt) REVERT: A 211 GLU cc_start: 0.8134 (tt0) cc_final: 0.7796 (pt0) REVERT: B 632 ASP cc_start: 0.8095 (t0) cc_final: 0.7610 (t0) REVERT: B 661 LEU cc_start: 0.8718 (tp) cc_final: 0.8443 (mt) REVERT: C 7 SER cc_start: 0.8033 (p) cc_final: 0.7686 (p) REVERT: C 13 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6804 (mmmt) REVERT: C 21 SER cc_start: 0.8108 (p) cc_final: 0.7810 (t) REVERT: C 43 GLN cc_start: 0.7134 (tp40) cc_final: 0.6677 (mp10) REVERT: C 81 MET cc_start: 0.8174 (tmm) cc_final: 0.7538 (tmm) REVERT: D 23 THR cc_start: 0.7416 (p) cc_final: 0.7093 (t) REVERT: D 47 LYS cc_start: 0.7853 (tptp) cc_final: 0.7615 (tttm) REVERT: F 54 CYS cc_start: 0.5365 (p) cc_final: 0.5079 (p) REVERT: F 57 ASP cc_start: 0.7490 (t0) cc_final: 0.7055 (p0) REVERT: F 103 GLN cc_start: 0.7673 (mt0) cc_final: 0.7191 (tm-30) REVERT: F 164 GLU cc_start: 0.7433 (pm20) cc_final: 0.7053 (pm20) REVERT: G 632 ASP cc_start: 0.7971 (t70) cc_final: 0.7565 (t0) REVERT: G 659 ASP cc_start: 0.8256 (m-30) cc_final: 0.7836 (t70) REVERT: G 661 LEU cc_start: 0.8901 (tp) cc_final: 0.8453 (mt) REVERT: H 6 GLN cc_start: 0.8190 (mt0) cc_final: 0.7962 (mt0) REVERT: H 43 GLN cc_start: 0.7502 (tp-100) cc_final: 0.7223 (mp10) REVERT: H 84 ASN cc_start: 0.8305 (t0) cc_final: 0.8074 (t0) REVERT: I 20 ILE cc_start: 0.6997 (mt) cc_final: 0.6768 (mt) REVERT: I 36 SER cc_start: 0.8999 (m) cc_final: 0.8661 (t) REVERT: I 38 TYR cc_start: 0.8144 (m-80) cc_final: 0.7405 (m-80) REVERT: I 63 ARG cc_start: 0.6853 (mtp-110) cc_final: 0.6401 (ptm-80) REVERT: I 107 LEU cc_start: 0.6976 (tp) cc_final: 0.6764 (tp) REVERT: K 103 GLN cc_start: 0.7720 (mt0) cc_final: 0.7505 (tm-30) REVERT: K 162 THR cc_start: 0.8326 (m) cc_final: 0.8117 (p) REVERT: K 207 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7678 (tttp) REVERT: L 584 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7872 (mt-10) REVERT: M 70 MET cc_start: 0.8894 (mtm) cc_final: 0.8609 (mtm) outliers start: 58 outliers final: 35 residues processed: 454 average time/residue: 0.3183 time to fit residues: 220.6789 Evaluate side-chains 402 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 367 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 283 ILE Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain L residue 606 THR Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 160 optimal weight: 40.0000 chunk 197 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 362 ASN B 590 GLN B 630 GLN F 114 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 GLN I 6 GLN K 478 ASN L 590 GLN N 40 GLN N 41 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117076 restraints weight = 29760.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117217 restraints weight = 23968.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118409 restraints weight = 26320.088| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 20565 Z= 0.232 Angle : 0.755 10.080 28092 Z= 0.382 Chirality : 0.048 0.337 3289 Planarity : 0.005 0.057 3480 Dihedral : 10.126 71.835 3794 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.03 % Favored : 94.61 % Rotamer: Outliers : 3.16 % Allowed : 14.48 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2466 helix: -1.34 (0.25), residues: 393 sheet: -0.14 (0.19), residues: 678 loop : -1.05 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 45 HIS 0.005 0.001 HIS F 330 PHE 0.017 0.002 PHE F 376 TYR 0.024 0.002 TYR N 51 ARG 0.008 0.001 ARG I 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 12) link_NAG-ASN : angle 1.69260 ( 36) link_ALPHA1-6 : bond 0.00591 ( 6) link_ALPHA1-6 : angle 1.87343 ( 18) link_BETA1-4 : bond 0.00477 ( 21) link_BETA1-4 : angle 2.19291 ( 63) link_ALPHA1-2 : bond 0.00855 ( 11) link_ALPHA1-2 : angle 2.16045 ( 33) link_ALPHA1-3 : bond 0.00925 ( 6) link_ALPHA1-3 : angle 1.76531 ( 18) hydrogen bonds : bond 0.04697 ( 534) hydrogen bonds : angle 6.07088 ( 1419) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.91291 ( 84) covalent geometry : bond 0.00548 (20467) covalent geometry : angle 0.73441 (27840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7379 (tmtt) cc_final: 0.6745 (tmtt) REVERT: A 211 GLU cc_start: 0.8093 (tt0) cc_final: 0.7772 (pt0) REVERT: B 632 ASP cc_start: 0.8162 (t0) cc_final: 0.7630 (t0) REVERT: B 661 LEU cc_start: 0.8909 (tp) cc_final: 0.8457 (mt) REVERT: C 21 SER cc_start: 0.8266 (p) cc_final: 0.7958 (t) REVERT: C 38 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7852 (ttp80) REVERT: C 43 GLN cc_start: 0.6947 (tp40) cc_final: 0.6588 (mp10) REVERT: C 46 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: C 81 MET cc_start: 0.8049 (tmm) cc_final: 0.7577 (tmm) REVERT: D 23 THR cc_start: 0.7414 (p) cc_final: 0.7115 (t) REVERT: D 63 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6496 (ptm-80) REVERT: F 164 GLU cc_start: 0.7393 (pm20) cc_final: 0.7021 (pm20) REVERT: F 442 ASN cc_start: 0.8102 (p0) cc_final: 0.7779 (p0) REVERT: G 632 ASP cc_start: 0.7989 (t70) cc_final: 0.7564 (t0) REVERT: G 659 ASP cc_start: 0.8067 (m-30) cc_final: 0.7782 (t70) REVERT: G 661 LEU cc_start: 0.8795 (tp) cc_final: 0.8543 (mt) REVERT: H 13 LYS cc_start: 0.7074 (mmtt) cc_final: 0.6859 (mmmt) REVERT: H 21 SER cc_start: 0.7879 (p) cc_final: 0.7628 (t) REVERT: H 38 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8030 (ttp80) REVERT: H 43 GLN cc_start: 0.7457 (tp-100) cc_final: 0.7252 (mp10) REVERT: H 46 GLU cc_start: 0.8083 (pt0) cc_final: 0.7591 (pt0) REVERT: H 81 MET cc_start: 0.7560 (tmm) cc_final: 0.7139 (tmm) REVERT: H 90 ASP cc_start: 0.7966 (m-30) cc_final: 0.7680 (m-30) REVERT: I 36 SER cc_start: 0.9012 (m) cc_final: 0.8646 (t) REVERT: I 63 ARG cc_start: 0.6650 (mtp-110) cc_final: 0.6421 (ptm-80) REVERT: K 162 THR cc_start: 0.8432 (m) cc_final: 0.8204 (p) REVERT: K 207 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7705 (tttp) REVERT: L 584 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7804 (mt-10) REVERT: L 607 ASN cc_start: 0.8890 (t0) cc_final: 0.8445 (m-40) REVERT: M 21 SER cc_start: 0.8117 (p) cc_final: 0.7738 (t) REVERT: M 43 GLN cc_start: 0.7032 (tp-100) cc_final: 0.6603 (mp10) REVERT: M 70 MET cc_start: 0.8884 (mtm) cc_final: 0.8491 (mtm) REVERT: N 106 LYS cc_start: 0.7279 (tppt) cc_final: 0.6999 (tppt) outliers start: 68 outliers final: 50 residues processed: 430 average time/residue: 0.3101 time to fit residues: 203.9396 Evaluate side-chains 401 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 235 optimal weight: 6.9990 chunk 241 optimal weight: 30.0000 chunk 217 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN D 40 GLN F 114 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 GLN K 66 HIS K 362 ASN K 478 ASN L 658 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.153913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116636 restraints weight = 30361.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115998 restraints weight = 25722.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117310 restraints weight = 27910.256| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20565 Z= 0.236 Angle : 0.728 10.131 28092 Z= 0.367 Chirality : 0.048 0.338 3289 Planarity : 0.005 0.055 3480 Dihedral : 9.131 66.689 3794 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.11 % Favored : 94.53 % Rotamer: Outliers : 3.90 % Allowed : 17.27 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2466 helix: -1.21 (0.26), residues: 393 sheet: -0.22 (0.20), residues: 696 loop : -1.17 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 45 HIS 0.006 0.001 HIS K 330 PHE 0.018 0.002 PHE A 376 TYR 0.024 0.002 TYR N 51 ARG 0.009 0.001 ARG L 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 12) link_NAG-ASN : angle 1.61544 ( 36) link_ALPHA1-6 : bond 0.00519 ( 6) link_ALPHA1-6 : angle 1.83952 ( 18) link_BETA1-4 : bond 0.00458 ( 21) link_BETA1-4 : angle 2.07879 ( 63) link_ALPHA1-2 : bond 0.00559 ( 11) link_ALPHA1-2 : angle 2.05070 ( 33) link_ALPHA1-3 : bond 0.00829 ( 6) link_ALPHA1-3 : angle 2.03898 ( 18) hydrogen bonds : bond 0.04526 ( 534) hydrogen bonds : angle 5.93454 ( 1419) SS BOND : bond 0.00465 ( 42) SS BOND : angle 1.70458 ( 84) covalent geometry : bond 0.00562 (20467) covalent geometry : angle 0.70872 (27840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 375 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7964 (tt0) cc_final: 0.7649 (pt0) REVERT: B 632 ASP cc_start: 0.8156 (t0) cc_final: 0.7660 (t0) REVERT: B 661 LEU cc_start: 0.8859 (tp) cc_final: 0.8402 (mt) REVERT: C 21 SER cc_start: 0.8328 (p) cc_final: 0.8123 (t) REVERT: C 38 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7764 (ttp80) REVERT: C 43 GLN cc_start: 0.7224 (tp40) cc_final: 0.6923 (mp10) REVERT: C 46 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: C 81 MET cc_start: 0.7859 (tmm) cc_final: 0.7430 (tmm) REVERT: C 90 ASP cc_start: 0.8022 (m-30) cc_final: 0.7578 (m-30) REVERT: D 23 THR cc_start: 0.7314 (p) cc_final: 0.7065 (t) REVERT: D 63 ARG cc_start: 0.6750 (mtp-110) cc_final: 0.6187 (ptm-80) REVERT: F 207 LYS cc_start: 0.7644 (mtpp) cc_final: 0.7410 (tttm) REVERT: G 632 ASP cc_start: 0.8026 (t70) cc_final: 0.7644 (t0) REVERT: G 659 ASP cc_start: 0.7983 (m-30) cc_final: 0.7765 (t70) REVERT: G 661 LEU cc_start: 0.8777 (tp) cc_final: 0.8517 (mt) REVERT: H 43 GLN cc_start: 0.7508 (tp-100) cc_final: 0.7173 (mp10) REVERT: H 81 MET cc_start: 0.7736 (tmm) cc_final: 0.7322 (tmm) REVERT: H 90 ASP cc_start: 0.8128 (m-30) cc_final: 0.7795 (m-30) REVERT: I 23 THR cc_start: 0.7332 (p) cc_final: 0.6949 (t) REVERT: I 36 SER cc_start: 0.9024 (m) cc_final: 0.8628 (t) REVERT: I 63 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6393 (ptm-80) REVERT: I 68 LYS cc_start: 0.7491 (tttt) cc_final: 0.6899 (tttp) REVERT: I 84 ASP cc_start: 0.6243 (m-30) cc_final: 0.5301 (m-30) REVERT: I 106 LYS cc_start: 0.8253 (tppt) cc_final: 0.7948 (tppt) REVERT: K 162 THR cc_start: 0.8504 (m) cc_final: 0.8232 (p) REVERT: K 207 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7683 (tttp) REVERT: L 584 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7865 (mt-10) REVERT: L 607 ASN cc_start: 0.8786 (t0) cc_final: 0.8478 (m-40) REVERT: N 106 LYS cc_start: 0.7379 (tppt) cc_final: 0.7072 (tppt) outliers start: 84 outliers final: 56 residues processed: 428 average time/residue: 0.3404 time to fit residues: 224.5500 Evaluate side-chains 393 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 56 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 137 optimal weight: 0.0570 chunk 213 optimal weight: 0.4980 chunk 105 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 128 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 overall best weight: 1.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN B 616 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN G 630 GLN G 656 ASN I 6 GLN N 6 GLN N 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118275 restraints weight = 30084.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118839 restraints weight = 23370.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119570 restraints weight = 26638.598| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20565 Z= 0.138 Angle : 0.656 11.597 28092 Z= 0.330 Chirality : 0.045 0.343 3289 Planarity : 0.004 0.051 3480 Dihedral : 8.125 58.887 3794 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.50 % Favored : 95.17 % Rotamer: Outliers : 3.06 % Allowed : 18.52 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2466 helix: -1.06 (0.26), residues: 393 sheet: -0.02 (0.20), residues: 693 loop : -1.09 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 614 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 210 TYR 0.025 0.001 TYR N 51 ARG 0.006 0.001 ARG B 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 12) link_NAG-ASN : angle 2.03552 ( 36) link_ALPHA1-6 : bond 0.00676 ( 6) link_ALPHA1-6 : angle 1.70893 ( 18) link_BETA1-4 : bond 0.00432 ( 21) link_BETA1-4 : angle 1.71068 ( 63) link_ALPHA1-2 : bond 0.00653 ( 11) link_ALPHA1-2 : angle 2.06493 ( 33) link_ALPHA1-3 : bond 0.01156 ( 6) link_ALPHA1-3 : angle 1.98570 ( 18) hydrogen bonds : bond 0.03960 ( 534) hydrogen bonds : angle 5.57287 ( 1419) SS BOND : bond 0.00304 ( 42) SS BOND : angle 1.24317 ( 84) covalent geometry : bond 0.00317 (20467) covalent geometry : angle 0.63881 (27840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 367 time to evaluate : 2.030 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 57 ASP cc_start: 0.7131 (m-30) cc_final: 0.6639 (p0) REVERT: A 104 MET cc_start: 0.8443 (ttt) cc_final: 0.8110 (ttt) REVERT: A 211 GLU cc_start: 0.7871 (tt0) cc_final: 0.7528 (pt0) REVERT: B 632 ASP cc_start: 0.8089 (t0) cc_final: 0.7547 (t0) REVERT: B 659 ASP cc_start: 0.8201 (m-30) cc_final: 0.7744 (t70) REVERT: B 661 LEU cc_start: 0.8698 (tp) cc_final: 0.8264 (mt) REVERT: C 21 SER cc_start: 0.8355 (p) cc_final: 0.8131 (t) REVERT: C 43 GLN cc_start: 0.7285 (tp40) cc_final: 0.6981 (mp10) REVERT: C 81 MET cc_start: 0.7855 (tmm) cc_final: 0.7444 (tmm) REVERT: C 90 ASP cc_start: 0.8025 (m-30) cc_final: 0.7612 (m-30) REVERT: D 63 ARG cc_start: 0.6824 (mtp-110) cc_final: 0.6371 (ptm-80) REVERT: F 57 ASP cc_start: 0.7111 (m-30) cc_final: 0.6399 (p0) REVERT: F 112 TRP cc_start: 0.8058 (t-100) cc_final: 0.7817 (t-100) REVERT: F 207 LYS cc_start: 0.7685 (mtpp) cc_final: 0.7418 (ttmm) REVERT: F 252 ARG cc_start: 0.8325 (mmt90) cc_final: 0.7934 (mtt90) REVERT: G 632 ASP cc_start: 0.7921 (t70) cc_final: 0.7534 (t0) REVERT: G 647 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: G 661 LEU cc_start: 0.8714 (tp) cc_final: 0.8433 (mt) REVERT: H 73 ASP cc_start: 0.8221 (m-30) cc_final: 0.7968 (m-30) REVERT: H 81 MET cc_start: 0.7660 (tmm) cc_final: 0.7235 (tmm) REVERT: I 20 ILE cc_start: 0.7154 (mt) cc_final: 0.6814 (mt) REVERT: I 23 THR cc_start: 0.7385 (p) cc_final: 0.7042 (t) REVERT: I 36 SER cc_start: 0.8991 (m) cc_final: 0.8617 (t) REVERT: I 42 PRO cc_start: 0.8394 (Cg_exo) cc_final: 0.8175 (Cg_endo) REVERT: I 63 ARG cc_start: 0.6575 (mtp-110) cc_final: 0.6242 (ptm-80) REVERT: I 68 LYS cc_start: 0.7512 (tttt) cc_final: 0.6914 (tttp) REVERT: I 84 ASP cc_start: 0.6335 (m-30) cc_final: 0.5376 (m-30) REVERT: I 106 LYS cc_start: 0.8219 (tppt) cc_final: 0.7941 (tppt) REVERT: K 162 THR cc_start: 0.8487 (m) cc_final: 0.8221 (p) REVERT: K 207 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7550 (tttp) REVERT: L 584 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7930 (mt-10) REVERT: L 607 ASN cc_start: 0.8768 (t0) cc_final: 0.8487 (m-40) REVERT: M 70 MET cc_start: 0.8968 (mtm) cc_final: 0.8670 (mtm) REVERT: N 6 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5983 (pt0) REVERT: N 62 ASN cc_start: 0.8628 (t0) cc_final: 0.8338 (t0) REVERT: N 106 LYS cc_start: 0.7511 (tppt) cc_final: 0.7256 (tppt) outliers start: 66 outliers final: 46 residues processed: 414 average time/residue: 0.3911 time to fit residues: 246.5282 Evaluate side-chains 386 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 637 ASN Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 38 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN F 343 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN I 6 GLN K 103 GLN K 343 GLN L 616 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115312 restraints weight = 30131.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114202 restraints weight = 24952.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115265 restraints weight = 28971.302| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20565 Z= 0.209 Angle : 0.688 12.937 28092 Z= 0.346 Chirality : 0.046 0.336 3289 Planarity : 0.005 0.050 3480 Dihedral : 7.984 59.275 3794 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.68 % Favored : 93.96 % Rotamer: Outliers : 4.04 % Allowed : 18.52 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2466 helix: -0.99 (0.26), residues: 393 sheet: -0.06 (0.20), residues: 696 loop : -1.17 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 614 HIS 0.005 0.001 HIS A 330 PHE 0.015 0.002 PHE F 376 TYR 0.023 0.002 TYR N 51 ARG 0.007 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 1.78107 ( 36) link_ALPHA1-6 : bond 0.00560 ( 6) link_ALPHA1-6 : angle 1.81150 ( 18) link_BETA1-4 : bond 0.00450 ( 21) link_BETA1-4 : angle 1.78270 ( 63) link_ALPHA1-2 : bond 0.00592 ( 11) link_ALPHA1-2 : angle 2.09178 ( 33) link_ALPHA1-3 : bond 0.00834 ( 6) link_ALPHA1-3 : angle 1.87794 ( 18) hydrogen bonds : bond 0.04141 ( 534) hydrogen bonds : angle 5.60818 ( 1419) SS BOND : bond 0.00385 ( 42) SS BOND : angle 1.47399 ( 84) covalent geometry : bond 0.00498 (20467) covalent geometry : angle 0.67049 (27840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 357 time to evaluate : 3.278 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: symmetry clash REVERT: A 57 ASP cc_start: 0.7230 (m-30) cc_final: 0.6679 (p0) REVERT: A 104 MET cc_start: 0.8462 (ttt) cc_final: 0.8147 (ttt) REVERT: A 207 LYS cc_start: 0.7835 (tptm) cc_final: 0.7513 (tptt) REVERT: A 211 GLU cc_start: 0.7944 (tt0) cc_final: 0.7561 (pt0) REVERT: B 626 MET cc_start: 0.7461 (ttp) cc_final: 0.7164 (ttm) REVERT: B 632 ASP cc_start: 0.8210 (t0) cc_final: 0.7694 (t0) REVERT: B 659 ASP cc_start: 0.8094 (m-30) cc_final: 0.7705 (t70) REVERT: B 661 LEU cc_start: 0.8693 (tp) cc_final: 0.8275 (mt) REVERT: C 21 SER cc_start: 0.8405 (p) cc_final: 0.8181 (t) REVERT: C 43 GLN cc_start: 0.7302 (tp40) cc_final: 0.6826 (mp10) REVERT: C 81 MET cc_start: 0.7894 (tmm) cc_final: 0.7507 (tmm) REVERT: C 83 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6854 (tt) REVERT: C 84 ASN cc_start: 0.8390 (t0) cc_final: 0.8149 (t0) REVERT: C 90 ASP cc_start: 0.7848 (m-30) cc_final: 0.7446 (m-30) REVERT: D 42 PRO cc_start: 0.8624 (Cg_exo) cc_final: 0.8311 (Cg_endo) REVERT: D 106 LYS cc_start: 0.7869 (tppt) cc_final: 0.7587 (tppt) REVERT: F 57 ASP cc_start: 0.7222 (m-30) cc_final: 0.6985 (m-30) REVERT: F 112 TRP cc_start: 0.8200 (t-100) cc_final: 0.7969 (t-100) REVERT: F 207 LYS cc_start: 0.7722 (mtpp) cc_final: 0.7441 (ttmm) REVERT: G 584 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7612 (mt-10) REVERT: G 632 ASP cc_start: 0.8006 (t70) cc_final: 0.7615 (t0) REVERT: H 13 LYS cc_start: 0.8394 (pptt) cc_final: 0.7531 (mmmt) REVERT: H 73 ASP cc_start: 0.8247 (m-30) cc_final: 0.7949 (m-30) REVERT: H 81 MET cc_start: 0.7711 (tmm) cc_final: 0.7304 (tmm) REVERT: I 20 ILE cc_start: 0.6927 (mt) cc_final: 0.6659 (mt) REVERT: I 23 THR cc_start: 0.7632 (p) cc_final: 0.7303 (t) REVERT: I 36 SER cc_start: 0.8986 (m) cc_final: 0.8643 (t) REVERT: I 42 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: I 63 ARG cc_start: 0.6603 (mtp-110) cc_final: 0.6298 (ptm-80) REVERT: I 84 ASP cc_start: 0.6284 (m-30) cc_final: 0.5377 (m-30) REVERT: K 162 THR cc_start: 0.8557 (m) cc_final: 0.8294 (p) REVERT: K 207 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7518 (tptp) REVERT: L 584 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: L 632 ASP cc_start: 0.8264 (t70) cc_final: 0.7859 (t0) REVERT: M 90 ASP cc_start: 0.7855 (m-30) cc_final: 0.7375 (m-30) REVERT: N 6 GLN cc_start: 0.5714 (OUTLIER) cc_final: 0.5372 (pt0) outliers start: 87 outliers final: 67 residues processed: 412 average time/residue: 0.3714 time to fit residues: 241.7387 Evaluate side-chains 409 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 339 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 4 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 188 optimal weight: 0.0010 chunk 21 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 100 optimal weight: 40.0000 chunk 223 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114647 restraints weight = 30252.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113897 restraints weight = 25772.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114915 restraints weight = 28353.761| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20565 Z= 0.238 Angle : 0.719 13.608 28092 Z= 0.362 Chirality : 0.047 0.334 3289 Planarity : 0.005 0.049 3480 Dihedral : 7.938 60.114 3794 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.24 % Favored : 93.39 % Rotamer: Outliers : 4.04 % Allowed : 18.90 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2466 helix: -0.96 (0.26), residues: 393 sheet: -0.12 (0.20), residues: 696 loop : -1.25 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 614 HIS 0.006 0.001 HIS M 35 PHE 0.018 0.002 PHE F 376 TYR 0.023 0.002 TYR N 51 ARG 0.008 0.001 ARG L 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 12) link_NAG-ASN : angle 1.77561 ( 36) link_ALPHA1-6 : bond 0.00511 ( 6) link_ALPHA1-6 : angle 1.84626 ( 18) link_BETA1-4 : bond 0.00442 ( 21) link_BETA1-4 : angle 1.83358 ( 63) link_ALPHA1-2 : bond 0.00590 ( 11) link_ALPHA1-2 : angle 2.09816 ( 33) link_ALPHA1-3 : bond 0.00697 ( 6) link_ALPHA1-3 : angle 1.79911 ( 18) hydrogen bonds : bond 0.04283 ( 534) hydrogen bonds : angle 5.69244 ( 1419) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.56523 ( 84) covalent geometry : bond 0.00568 (20467) covalent geometry : angle 0.70266 (27840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 346 time to evaluate : 2.252 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 104 MET cc_start: 0.8459 (ttt) cc_final: 0.8149 (ttt) REVERT: A 207 LYS cc_start: 0.7920 (tptm) cc_final: 0.7563 (tptp) REVERT: A 211 GLU cc_start: 0.7949 (tt0) cc_final: 0.7606 (pt0) REVERT: B 626 MET cc_start: 0.7493 (ttp) cc_final: 0.7201 (ttm) REVERT: B 632 ASP cc_start: 0.8279 (t0) cc_final: 0.7806 (t0) REVERT: B 659 ASP cc_start: 0.8063 (m-30) cc_final: 0.7698 (t70) REVERT: B 661 LEU cc_start: 0.8748 (tp) cc_final: 0.8293 (mt) REVERT: C 3 GLN cc_start: 0.8409 (tp40) cc_final: 0.8202 (tp40) REVERT: C 81 MET cc_start: 0.7943 (tmm) cc_final: 0.7570 (tmm) REVERT: C 83 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6797 (tt) REVERT: C 84 ASN cc_start: 0.8384 (t0) cc_final: 0.8103 (t0) REVERT: C 90 ASP cc_start: 0.7869 (m-30) cc_final: 0.7395 (m-30) REVERT: D 42 PRO cc_start: 0.8651 (Cg_exo) cc_final: 0.8339 (Cg_endo) REVERT: D 63 ARG cc_start: 0.6992 (mtm110) cc_final: 0.6637 (ptm-80) REVERT: D 106 LYS cc_start: 0.8099 (tppt) cc_final: 0.7891 (tppt) REVERT: F 95 MET cc_start: 0.7245 (ttp) cc_final: 0.6947 (ttp) REVERT: F 207 LYS cc_start: 0.7747 (mtpp) cc_final: 0.7473 (ttmm) REVERT: F 502 LYS cc_start: 0.8639 (ptmt) cc_final: 0.8301 (ttpt) REVERT: G 638 TYR cc_start: 0.7801 (m-10) cc_final: 0.7569 (m-10) REVERT: H 13 LYS cc_start: 0.8406 (pptt) cc_final: 0.7568 (mmmt) REVERT: H 43 GLN cc_start: 0.7541 (mp10) cc_final: 0.7276 (mp10) REVERT: H 73 ASP cc_start: 0.8197 (m-30) cc_final: 0.7933 (m-30) REVERT: H 81 MET cc_start: 0.7747 (tmm) cc_final: 0.7323 (tmm) REVERT: I 20 ILE cc_start: 0.6887 (mt) cc_final: 0.6631 (mt) REVERT: I 23 THR cc_start: 0.7613 (p) cc_final: 0.7270 (t) REVERT: I 36 SER cc_start: 0.8958 (m) cc_final: 0.8669 (t) REVERT: I 106 LYS cc_start: 0.8389 (tppt) cc_final: 0.8167 (tppt) REVERT: K 162 THR cc_start: 0.8600 (m) cc_final: 0.8336 (p) REVERT: K 207 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7543 (tptp) REVERT: K 475 MET cc_start: 0.7447 (mmm) cc_final: 0.7171 (mmt) REVERT: L 584 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: L 607 ASN cc_start: 0.8832 (m-40) cc_final: 0.8356 (m-40) REVERT: L 629 LEU cc_start: 0.7342 (tt) cc_final: 0.7077 (mt) REVERT: L 632 ASP cc_start: 0.8159 (t70) cc_final: 0.7793 (t0) REVERT: M 70 MET cc_start: 0.8941 (mtm) cc_final: 0.8454 (mtm) REVERT: M 90 ASP cc_start: 0.7917 (m-30) cc_final: 0.7498 (m-30) REVERT: N 6 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5999 (pt0) outliers start: 87 outliers final: 72 residues processed: 406 average time/residue: 0.3182 time to fit residues: 198.9559 Evaluate side-chains 404 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 329 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 602 LEU Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 236 optimal weight: 50.0000 chunk 227 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 184 optimal weight: 9.9990 chunk 47 optimal weight: 0.0010 chunk 127 optimal weight: 6.9990 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 62 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN L 630 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122996 restraints weight = 29260.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122402 restraints weight = 30359.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124170 restraints weight = 26806.882| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20565 Z= 0.137 Angle : 0.657 12.929 28092 Z= 0.329 Chirality : 0.045 0.340 3289 Planarity : 0.004 0.049 3480 Dihedral : 7.344 55.253 3794 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.27 % Favored : 94.40 % Rotamer: Outliers : 3.11 % Allowed : 20.57 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2466 helix: -0.80 (0.26), residues: 393 sheet: 0.01 (0.20), residues: 675 loop : -1.18 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 628 HIS 0.004 0.001 HIS M 35 PHE 0.010 0.001 PHE F 391 TYR 0.025 0.001 TYR N 51 ARG 0.008 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 12) link_NAG-ASN : angle 1.41228 ( 36) link_ALPHA1-6 : bond 0.00683 ( 6) link_ALPHA1-6 : angle 1.70658 ( 18) link_BETA1-4 : bond 0.00387 ( 21) link_BETA1-4 : angle 1.56698 ( 63) link_ALPHA1-2 : bond 0.00599 ( 11) link_ALPHA1-2 : angle 2.09242 ( 33) link_ALPHA1-3 : bond 0.00937 ( 6) link_ALPHA1-3 : angle 1.62153 ( 18) hydrogen bonds : bond 0.03739 ( 534) hydrogen bonds : angle 5.40608 ( 1419) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.26174 ( 84) covalent geometry : bond 0.00318 (20467) covalent geometry : angle 0.64343 (27840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 355 time to evaluate : 2.934 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: symmetry clash REVERT: A 57 ASP cc_start: 0.7052 (m-30) cc_final: 0.6740 (p0) REVERT: A 104 MET cc_start: 0.8487 (ttt) cc_final: 0.8165 (ttt) REVERT: A 207 LYS cc_start: 0.7875 (tptm) cc_final: 0.7533 (tptp) REVERT: A 211 GLU cc_start: 0.7920 (tt0) cc_final: 0.7546 (pt0) REVERT: B 632 ASP cc_start: 0.8153 (t0) cc_final: 0.7680 (t0) REVERT: B 659 ASP cc_start: 0.8052 (m-30) cc_final: 0.7746 (t70) REVERT: B 661 LEU cc_start: 0.8755 (tp) cc_final: 0.8229 (mt) REVERT: C 81 MET cc_start: 0.7829 (tmm) cc_final: 0.7442 (tmm) REVERT: C 83 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6903 (tt) REVERT: C 84 ASN cc_start: 0.8310 (t0) cc_final: 0.8030 (t0) REVERT: C 90 ASP cc_start: 0.7841 (m-30) cc_final: 0.7386 (m-30) REVERT: D 42 PRO cc_start: 0.8605 (Cg_exo) cc_final: 0.8322 (Cg_endo) REVERT: F 57 ASP cc_start: 0.7170 (m-30) cc_final: 0.6564 (p0) REVERT: F 91 GLU cc_start: 0.6266 (tp30) cc_final: 0.5930 (tp30) REVERT: F 95 MET cc_start: 0.7155 (ttp) cc_final: 0.6858 (ttp) REVERT: F 207 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7403 (ttmm) REVERT: F 283 ILE cc_start: 0.8804 (mt) cc_final: 0.8453 (tt) REVERT: F 502 LYS cc_start: 0.8500 (ptmt) cc_final: 0.8225 (ttpt) REVERT: G 610 TRP cc_start: 0.7664 (t-100) cc_final: 0.7335 (t-100) REVERT: G 629 LEU cc_start: 0.7398 (tt) cc_final: 0.6978 (mt) REVERT: H 13 LYS cc_start: 0.8305 (pptt) cc_final: 0.7544 (mmmt) REVERT: H 73 ASP cc_start: 0.8119 (m-30) cc_final: 0.7890 (m-30) REVERT: H 81 MET cc_start: 0.7612 (tmm) cc_final: 0.7203 (tmm) REVERT: I 20 ILE cc_start: 0.6727 (mt) cc_final: 0.6409 (mt) REVERT: I 36 SER cc_start: 0.8843 (m) cc_final: 0.8617 (t) REVERT: I 106 LYS cc_start: 0.8394 (tppt) cc_final: 0.8171 (tppt) REVERT: K 207 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7572 (tptp) REVERT: L 584 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: L 607 ASN cc_start: 0.8725 (m-40) cc_final: 0.8289 (m-40) REVERT: L 629 LEU cc_start: 0.7303 (tt) cc_final: 0.7084 (mt) REVERT: L 632 ASP cc_start: 0.8067 (t70) cc_final: 0.7671 (t0) REVERT: M 70 MET cc_start: 0.9012 (mtm) cc_final: 0.8513 (mtm) REVERT: M 90 ASP cc_start: 0.7971 (m-30) cc_final: 0.7639 (m-30) outliers start: 67 outliers final: 59 residues processed: 403 average time/residue: 0.3817 time to fit residues: 241.1630 Evaluate side-chains 393 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 332 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 243 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 200 optimal weight: 40.0000 chunk 168 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN G 590 GLN I 6 GLN M 43 GLN N 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.149182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111671 restraints weight = 30270.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111103 restraints weight = 25034.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111844 restraints weight = 28998.399| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20565 Z= 0.301 Angle : 0.791 13.985 28092 Z= 0.398 Chirality : 0.049 0.330 3289 Planarity : 0.005 0.055 3480 Dihedral : 7.968 61.431 3794 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.34 % Favored : 92.30 % Rotamer: Outliers : 3.99 % Allowed : 20.01 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2466 helix: -0.95 (0.26), residues: 393 sheet: -0.29 (0.20), residues: 684 loop : -1.36 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 628 HIS 0.007 0.001 HIS M 35 PHE 0.021 0.002 PHE F 376 TYR 0.022 0.002 TYR D 51 ARG 0.007 0.001 ARG B 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 12) link_NAG-ASN : angle 2.00537 ( 36) link_ALPHA1-6 : bond 0.00444 ( 6) link_ALPHA1-6 : angle 1.90214 ( 18) link_BETA1-4 : bond 0.00491 ( 21) link_BETA1-4 : angle 1.98792 ( 63) link_ALPHA1-2 : bond 0.00548 ( 11) link_ALPHA1-2 : angle 2.13462 ( 33) link_ALPHA1-3 : bond 0.00771 ( 6) link_ALPHA1-3 : angle 1.85768 ( 18) hydrogen bonds : bond 0.04615 ( 534) hydrogen bonds : angle 5.78809 ( 1419) SS BOND : bond 0.00520 ( 42) SS BOND : angle 1.83700 ( 84) covalent geometry : bond 0.00721 (20467) covalent geometry : angle 0.77278 (27840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 340 time to evaluate : 2.243 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 104 MET cc_start: 0.8518 (ttt) cc_final: 0.8189 (ttt) REVERT: A 207 LYS cc_start: 0.8038 (tptm) cc_final: 0.7812 (tptt) REVERT: A 211 GLU cc_start: 0.7926 (tt0) cc_final: 0.7636 (pt0) REVERT: B 607 ASN cc_start: 0.8734 (t0) cc_final: 0.8289 (m-40) REVERT: B 610 TRP cc_start: 0.7220 (t-100) cc_final: 0.6969 (t-100) REVERT: B 632 ASP cc_start: 0.8359 (t0) cc_final: 0.7845 (t0) REVERT: B 659 ASP cc_start: 0.8036 (m-30) cc_final: 0.7744 (t70) REVERT: B 661 LEU cc_start: 0.8746 (tp) cc_final: 0.8268 (mt) REVERT: C 23 LYS cc_start: 0.8652 (tttt) cc_final: 0.8340 (mmtt) REVERT: C 81 MET cc_start: 0.8053 (tmm) cc_final: 0.7807 (tmm) REVERT: C 83 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6706 (tt) REVERT: C 84 ASN cc_start: 0.8459 (t0) cc_final: 0.8207 (t0) REVERT: D 42 PRO cc_start: 0.8687 (Cg_exo) cc_final: 0.8395 (Cg_endo) REVERT: F 91 GLU cc_start: 0.6394 (tp30) cc_final: 0.6020 (tp30) REVERT: F 95 MET cc_start: 0.7159 (ttp) cc_final: 0.6899 (ttp) REVERT: F 207 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7475 (ttmm) REVERT: F 283 ILE cc_start: 0.8817 (mt) cc_final: 0.8388 (tt) REVERT: G 610 TRP cc_start: 0.7654 (t-100) cc_final: 0.7330 (t-100) REVERT: H 13 LYS cc_start: 0.8347 (pptt) cc_final: 0.7602 (mmmt) REVERT: H 73 ASP cc_start: 0.8146 (m-30) cc_final: 0.7865 (m-30) REVERT: H 81 MET cc_start: 0.7988 (tmm) cc_final: 0.7594 (tmm) REVERT: I 20 ILE cc_start: 0.6977 (mt) cc_final: 0.6704 (mt) REVERT: I 36 SER cc_start: 0.8902 (m) cc_final: 0.8627 (t) REVERT: I 63 ARG cc_start: 0.6174 (ptm160) cc_final: 0.5910 (ptm-80) REVERT: I 106 LYS cc_start: 0.8510 (tppt) cc_final: 0.8265 (tppt) REVERT: K 57 ASP cc_start: 0.7761 (m-30) cc_final: 0.7319 (m-30) REVERT: K 207 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7539 (tptp) REVERT: L 530 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7056 (mtp) REVERT: L 584 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: L 607 ASN cc_start: 0.8834 (m-40) cc_final: 0.8374 (m-40) REVERT: L 629 LEU cc_start: 0.7358 (tt) cc_final: 0.7053 (mt) REVERT: L 632 ASP cc_start: 0.8114 (t70) cc_final: 0.7783 (t0) REVERT: M 90 ASP cc_start: 0.7949 (m-30) cc_final: 0.7644 (m-30) outliers start: 86 outliers final: 71 residues processed: 398 average time/residue: 0.3462 time to fit residues: 211.0240 Evaluate side-chains 405 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 330 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 602 LEU Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 225 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.153542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115974 restraints weight = 30150.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115538 restraints weight = 23411.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117337 restraints weight = 20916.109| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20565 Z= 0.143 Angle : 0.683 13.844 28092 Z= 0.342 Chirality : 0.045 0.340 3289 Planarity : 0.004 0.048 3480 Dihedral : 7.280 55.604 3794 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.70 % Favored : 94.97 % Rotamer: Outliers : 2.92 % Allowed : 21.49 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2466 helix: -0.74 (0.26), residues: 393 sheet: 0.01 (0.21), residues: 627 loop : -1.29 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 628 HIS 0.004 0.001 HIS K 374 PHE 0.009 0.001 PHE K 93 TYR 0.026 0.001 TYR N 51 ARG 0.009 0.001 ARG L 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 12) link_NAG-ASN : angle 1.41207 ( 36) link_ALPHA1-6 : bond 0.00704 ( 6) link_ALPHA1-6 : angle 1.71918 ( 18) link_BETA1-4 : bond 0.00364 ( 21) link_BETA1-4 : angle 1.55075 ( 63) link_ALPHA1-2 : bond 0.00619 ( 11) link_ALPHA1-2 : angle 2.11916 ( 33) link_ALPHA1-3 : bond 0.00979 ( 6) link_ALPHA1-3 : angle 1.56577 ( 18) hydrogen bonds : bond 0.03795 ( 534) hydrogen bonds : angle 5.38888 ( 1419) SS BOND : bond 0.00320 ( 42) SS BOND : angle 1.27397 ( 84) covalent geometry : bond 0.00333 (20467) covalent geometry : angle 0.66957 (27840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 345 time to evaluate : 2.338 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 57 ASP cc_start: 0.7084 (m-30) cc_final: 0.6538 (p0) REVERT: A 104 MET cc_start: 0.8466 (ttt) cc_final: 0.8140 (ttt) REVERT: A 211 GLU cc_start: 0.7918 (tt0) cc_final: 0.7557 (pt0) REVERT: B 607 ASN cc_start: 0.8662 (t0) cc_final: 0.8181 (m-40) REVERT: B 610 TRP cc_start: 0.7278 (t-100) cc_final: 0.7034 (t-100) REVERT: B 629 LEU cc_start: 0.7757 (tp) cc_final: 0.7451 (mt) REVERT: B 632 ASP cc_start: 0.8309 (t0) cc_final: 0.7778 (t0) REVERT: B 659 ASP cc_start: 0.8036 (m-30) cc_final: 0.7733 (t70) REVERT: C 23 LYS cc_start: 0.8563 (tttt) cc_final: 0.8283 (mmtt) REVERT: C 38 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7948 (ttp80) REVERT: C 81 MET cc_start: 0.8092 (tmm) cc_final: 0.7725 (tmm) REVERT: C 83 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6565 (tt) REVERT: C 84 ASN cc_start: 0.8452 (t0) cc_final: 0.8244 (t0) REVERT: D 42 PRO cc_start: 0.8696 (Cg_exo) cc_final: 0.8396 (Cg_endo) REVERT: D 63 ARG cc_start: 0.7347 (mtm110) cc_final: 0.6490 (ttp80) REVERT: F 57 ASP cc_start: 0.7173 (m-30) cc_final: 0.6565 (p0) REVERT: F 91 GLU cc_start: 0.6355 (tp30) cc_final: 0.5948 (tp30) REVERT: F 95 MET cc_start: 0.7054 (ttp) cc_final: 0.6728 (ttp) REVERT: F 283 ILE cc_start: 0.8824 (mt) cc_final: 0.8398 (tt) REVERT: G 629 LEU cc_start: 0.7456 (tt) cc_final: 0.6980 (mp) REVERT: H 13 LYS cc_start: 0.8375 (pptt) cc_final: 0.7688 (mmmt) REVERT: H 73 ASP cc_start: 0.8187 (m-30) cc_final: 0.7937 (m-30) REVERT: H 81 MET cc_start: 0.7839 (tmm) cc_final: 0.7349 (tmm) REVERT: I 20 ILE cc_start: 0.6684 (mt) cc_final: 0.6387 (mt) REVERT: I 36 SER cc_start: 0.8912 (m) cc_final: 0.8562 (t) REVERT: I 106 LYS cc_start: 0.8558 (tppt) cc_final: 0.8342 (tppt) REVERT: K 57 ASP cc_start: 0.7703 (m-30) cc_final: 0.7262 (m-30) REVERT: K 207 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7504 (tptp) REVERT: K 276 ASN cc_start: 0.6520 (t0) cc_final: 0.5880 (p0) REVERT: K 475 MET cc_start: 0.7101 (mmm) cc_final: 0.6872 (mmt) REVERT: L 584 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: L 607 ASN cc_start: 0.8848 (m-40) cc_final: 0.8399 (m-40) REVERT: L 617 ARG cc_start: 0.7660 (tmt-80) cc_final: 0.7382 (tmt-80) REVERT: M 70 MET cc_start: 0.9051 (mtm) cc_final: 0.8439 (mtm) REVERT: M 90 ASP cc_start: 0.7899 (m-30) cc_final: 0.7551 (m-30) outliers start: 63 outliers final: 60 residues processed: 388 average time/residue: 0.3330 time to fit residues: 194.8138 Evaluate side-chains 398 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 370 GLU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 156 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.150856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114182 restraints weight = 30511.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114246 restraints weight = 26526.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115083 restraints weight = 29856.896| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20565 Z= 0.231 Angle : 0.736 14.049 28092 Z= 0.367 Chirality : 0.047 0.333 3289 Planarity : 0.005 0.062 3480 Dihedral : 7.447 57.829 3794 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.41 % Favored : 93.23 % Rotamer: Outliers : 3.57 % Allowed : 21.12 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2466 helix: -0.81 (0.26), residues: 396 sheet: -0.15 (0.21), residues: 630 loop : -1.27 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 112 HIS 0.005 0.001 HIS A 330 PHE 0.018 0.002 PHE F 376 TYR 0.023 0.002 TYR N 51 ARG 0.010 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 12) link_NAG-ASN : angle 1.70140 ( 36) link_ALPHA1-6 : bond 0.00553 ( 6) link_ALPHA1-6 : angle 1.82563 ( 18) link_BETA1-4 : bond 0.00409 ( 21) link_BETA1-4 : angle 1.74447 ( 63) link_ALPHA1-2 : bond 0.00582 ( 11) link_ALPHA1-2 : angle 2.14487 ( 33) link_ALPHA1-3 : bond 0.00761 ( 6) link_ALPHA1-3 : angle 1.61132 ( 18) hydrogen bonds : bond 0.04106 ( 534) hydrogen bonds : angle 5.49935 ( 1419) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.49837 ( 84) covalent geometry : bond 0.00553 (20467) covalent geometry : angle 0.72097 (27840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7408.01 seconds wall clock time: 133 minutes 51.43 seconds (8031.43 seconds total)