Starting phenix.real_space_refine on Tue May 20 15:50:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aug_43879/05_2025/9aug_43879_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aug_43879/05_2025/9aug_43879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9aug_43879/05_2025/9aug_43879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aug_43879/05_2025/9aug_43879.map" model { file = "/net/cci-nas-00/data/ceres_data/9aug_43879/05_2025/9aug_43879_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aug_43879/05_2025/9aug_43879_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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 12591 2.51 5 N 3342 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20211 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "C" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "M" 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: "N" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.00, per 1000 atoms: 0.59 Number of scatterers: 20211 At special positions: 0 Unit cell: (146.88, 160.92, 157.68, 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 4143 8.00 N 3342 7.00 C 12591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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 218 " - pdb=" SG CYS A 247 " distance=2.05 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 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.05 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 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 N 4 " - " MAN N 5 " " MAN S 4 " - " MAN S 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 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 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 362 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 442 " " NAG B 601 " - " ASN B 386 " " NAG B 602 " - " ASN B 392 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 362 " " NAG B 605 " - " ASN B 276 " " NAG B 606 " - " ASN B 88 " " NAG B 607 " - " ASN B 241 " " NAG B 608 " - " ASN B 448 " " NAG B 609 " - " ASN B 442 " " NAG C 601 " - " ASN C 386 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 362 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 442 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 300 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN B 262 " " NAG S 1 " - " ASN B 332 " " NAG T 1 " - " ASN B 300 " " NAG U 1 " - " ASN B 156 " " NAG V 1 " - " ASN B 197 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 300 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 197 " Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 2.4 seconds 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 46 sheets defined 18.4% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.039A pdb=" N GLU A 62 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.852A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.710A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.735A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.511A pdb=" N ASN A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 409' Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.099A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.147A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.632A pdb=" N TYR B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.587A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.909A pdb=" N SER B 409 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 475 through 482 removed outlier: 4.351A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.580A pdb=" N ALA C 60 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 62 " --> pdb=" O ARG C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 62' Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.249A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.610A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.118A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.205A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.902A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.515A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.122A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.638A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.545A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.544A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.879A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR E 536 " --> pdb=" O ALA E 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 532 through 536' Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.175A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.713A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 636 " --> pdb=" O ASP E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 664 removed outlier: 3.623A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 removed outlier: 3.921A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 4.615A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.650A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.893A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 664 removed outlier: 3.964A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.070A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (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 removed outlier: 3.561A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.133A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.594A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.518A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.736A pdb=" N SER A 56 " --> pdb=" O VAL A 75 " (cutoff:3.500A) 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 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.540A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.614A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.366A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 294 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.625A pdb=" N LEU B 84 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 44 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 494 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL B 42 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N VAL B 496 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N TYR B 40 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N VAL B 38 " --> pdb=" O PRO B 498 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB7, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AB8, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.312A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 393 " --> pdb=" O TYR B 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 294 through 296 removed outlier: 3.886A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 384 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain 'C' and resid 83 through 85 removed outlier: 9.187A pdb=" N VAL C 489 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TRP C 45 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ILE C 491 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.600A pdb=" N SER C 56 " --> pdb=" O VAL C 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC7, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AC8, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.405A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.936A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.936A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY C 393 " --> pdb=" O TYR C 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 413 through 418 removed outlier: 4.003A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 294 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD4, first strand: chain 'C' and resid 374 through 378 Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.275A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN G 59 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.753A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 11 removed outlier: 5.339A pdb=" N TYR I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP I 50 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN I 59 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 9 through 12 removed outlier: 7.098A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AE4, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AE5, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AE6, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.681A pdb=" N MET K 49 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.681A pdb=" N MET K 49 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA K 86 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU K 107 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR K 88 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR K 105 " --> pdb=" O TYR K 88 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.699A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN L 39 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AF1, first strand: chain 'L' and resid 17 through 23 623 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.48 Time building geometry restraints manager: 6.81 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: 6362 1.35 - 1.48: 5486 1.48 - 1.61: 8590 1.61 - 1.74: 1 1.74 - 1.87: 183 Bond restraints: 20622 Sorted by residual: bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.331 1.378 -0.046 7.90e-03 1.60e+04 3.40e+01 bond pdb=" C1 NAG C 606 " pdb=" O5 NAG C 606 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" C1 MAN X 4 " pdb=" C2 MAN X 4 " ideal model delta sigma weight residual 1.526 1.579 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.30e+00 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 27000 2.41 - 4.82: 824 4.82 - 7.23: 153 7.23 - 9.64: 34 9.64 - 12.05: 9 Bond angle restraints: 28020 Sorted by residual: angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 125.88 -11.48 2.30e+00 1.89e-01 2.49e+01 angle pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " ideal model delta sigma weight residual 114.10 123.71 -9.61 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA CYS C 247 " pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 114.40 125.38 -10.98 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C SER E 615 " pdb=" N ASN E 616 " pdb=" CA ASN E 616 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN C 67 " pdb=" N VAL C 68 " pdb=" CA VAL C 68 " ideal model delta sigma weight residual 121.97 129.81 -7.84 1.80e+00 3.09e-01 1.90e+01 ... (remaining 28015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 12296 23.33 - 46.67: 865 46.67 - 70.00: 118 70.00 - 93.34: 83 93.34 - 116.67: 75 Dihedral angle restraints: 13437 sinusoidal: 6369 harmonic: 7068 Sorted by residual: dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual -86.00 -22.34 -63.66 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 49.25 43.75 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS B 385 " pdb=" SG CYS B 385 " pdb=" SG CYS B 418 " pdb=" CB CYS B 418 " ideal model delta sinusoidal sigma weight residual 93.00 49.46 43.54 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 13434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2771 0.073 - 0.147: 515 0.147 - 0.220: 73 0.220 - 0.294: 19 0.294 - 0.367: 6 Chirality restraints: 3384 Sorted by residual: chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 88 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 2.44 -0.04 2.00e-02 2.50e+03 3.29e+00 chirality pdb=" CB VAL C 430 " pdb=" CA VAL C 430 " pdb=" CG1 VAL C 430 " pdb=" CG2 VAL C 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3381 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 69 " 0.017 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP B 69 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 69 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 69 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 69 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 69 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 69 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.022 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP H 36 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 117 " -0.012 2.00e-02 2.50e+03 1.99e-02 9.88e+00 pdb=" CG TRP I 117 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP I 117 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP I 117 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 117 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP I 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 117 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 117 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 117 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP I 117 " 0.009 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4708 2.80 - 3.32: 16641 3.32 - 3.85: 31876 3.85 - 4.37: 33310 4.37 - 4.90: 60753 Nonbonded interactions: 147288 Sorted by model distance: nonbonded pdb=" OG1 THR E 627 " pdb=" OE1 GLN E 630 " model vdw 2.270 3.040 nonbonded pdb=" OG SER C 185 " pdb=" O THR C 185b" model vdw 2.285 3.040 nonbonded pdb=" OG SER B 256 " pdb=" O LEU B 259 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR L 5 " pdb=" OG1 THR L 23 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR F 627 " pdb=" OE1 GLN F 630 " model vdw 2.295 3.040 ... (remaining 147283 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 46.860 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.150 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:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 0.109 20745 Z= 0.280 Angle : 1.036 12.754 28353 Z= 0.504 Chirality : 0.061 0.367 3384 Planarity : 0.006 0.117 3456 Dihedral : 18.451 116.672 8811 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.15), residues: 2427 helix: -1.41 (0.22), residues: 375 sheet: -0.52 (0.21), residues: 615 loop : -2.55 (0.14), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP B 69 HIS 0.005 0.001 HIS C 374 PHE 0.029 0.002 PHE B 317 TYR 0.036 0.002 TYR C 486 ARG 0.018 0.001 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 3.61218 ( 126) link_ALPHA1-6 : bond 0.00364 ( 9) link_ALPHA1-6 : angle 1.52587 ( 27) link_BETA1-4 : bond 0.00720 ( 24) link_BETA1-4 : angle 1.98311 ( 72) link_ALPHA1-2 : bond 0.00541 ( 3) link_ALPHA1-2 : angle 2.95041 ( 9) link_ALPHA1-3 : bond 0.00537 ( 9) link_ALPHA1-3 : angle 1.60944 ( 27) hydrogen bonds : bond 0.14583 ( 604) hydrogen bonds : angle 6.58668 ( 1674) SS BOND : bond 0.00786 ( 36) SS BOND : angle 2.00405 ( 72) covalent geometry : bond 0.00583 (20622) covalent geometry : angle 0.99993 (28020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 647 GLU cc_start: 0.7513 (tt0) cc_final: 0.7279 (tt0) REVERT: E 538 THR cc_start: 0.9223 (p) cc_final: 0.8955 (p) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2958 time to fit residues: 183.9818 Evaluate side-chains 330 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 10.0000 chunk 184 optimal weight: 0.4980 chunk 102 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 656 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN K 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112425 restraints weight = 32796.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113200 restraints weight = 28946.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113999 restraints weight = 25786.827| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20745 Z= 0.183 Angle : 0.707 9.385 28353 Z= 0.338 Chirality : 0.047 0.392 3384 Planarity : 0.004 0.064 3456 Dihedral : 13.971 112.228 4413 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.79 % Allowed : 10.89 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2427 helix: -0.33 (0.27), residues: 399 sheet: -0.34 (0.21), residues: 627 loop : -2.42 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 36 HIS 0.006 0.001 HIS C 374 PHE 0.026 0.002 PHE B 317 TYR 0.023 0.002 TYR K 51 ARG 0.007 0.001 ARG I 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 42) link_NAG-ASN : angle 2.78182 ( 126) link_ALPHA1-6 : bond 0.00597 ( 9) link_ALPHA1-6 : angle 1.66615 ( 27) link_BETA1-4 : bond 0.00447 ( 24) link_BETA1-4 : angle 2.11546 ( 72) link_ALPHA1-2 : bond 0.00674 ( 3) link_ALPHA1-2 : angle 3.27832 ( 9) link_ALPHA1-3 : bond 0.00946 ( 9) link_ALPHA1-3 : angle 2.51326 ( 27) hydrogen bonds : bond 0.03713 ( 604) hydrogen bonds : angle 5.15371 ( 1674) SS BOND : bond 0.00744 ( 36) SS BOND : angle 1.07071 ( 72) covalent geometry : bond 0.00429 (20622) covalent geometry : angle 0.66685 (28020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 346 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8370 (tp) cc_final: 0.8004 (tt) REVERT: A 425 ASN cc_start: 0.7721 (t0) cc_final: 0.7490 (t0) REVERT: B 317 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8172 (p90) REVERT: C 475 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7686 (tpp) REVERT: C 504 ARG cc_start: 0.6243 (tmt170) cc_final: 0.5978 (tmt170) REVERT: D 540 GLN cc_start: 0.8259 (tt0) cc_final: 0.7885 (tm-30) REVERT: E 530 MET cc_start: 0.7040 (tpt) cc_final: 0.6534 (tpt) REVERT: E 538 THR cc_start: 0.9295 (p) cc_final: 0.9070 (p) REVERT: E 596 TRP cc_start: 0.7498 (p90) cc_final: 0.7115 (p90) REVERT: E 623 TRP cc_start: 0.7771 (m100) cc_final: 0.7317 (m100) REVERT: F 589 ASP cc_start: 0.8181 (t0) cc_final: 0.7883 (t0) REVERT: G 12 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7356 (mmmm) REVERT: G 73 ASP cc_start: 0.7876 (t0) cc_final: 0.7598 (t0) REVERT: G 115 ASP cc_start: 0.8304 (t0) cc_final: 0.7784 (t0) outliers start: 38 outliers final: 28 residues processed: 368 average time/residue: 0.2953 time to fit residues: 169.6308 Evaluate side-chains 350 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 320 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 145 optimal weight: 0.2980 chunk 218 optimal weight: 9.9990 chunk 30 optimal weight: 0.0270 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113809 restraints weight = 32641.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114677 restraints weight = 28251.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115598 restraints weight = 24524.560| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20745 Z= 0.118 Angle : 0.618 9.397 28353 Z= 0.299 Chirality : 0.045 0.360 3384 Planarity : 0.003 0.046 3456 Dihedral : 12.324 113.534 4413 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.60 % Allowed : 13.77 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.17), residues: 2427 helix: 0.41 (0.28), residues: 381 sheet: -0.35 (0.21), residues: 645 loop : -2.33 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 36 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.001 PHE B 317 TYR 0.016 0.001 TYR K 51 ARG 0.006 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 42) link_NAG-ASN : angle 2.62459 ( 126) link_ALPHA1-6 : bond 0.00680 ( 9) link_ALPHA1-6 : angle 1.57756 ( 27) link_BETA1-4 : bond 0.00523 ( 24) link_BETA1-4 : angle 1.75533 ( 72) link_ALPHA1-2 : bond 0.01034 ( 3) link_ALPHA1-2 : angle 2.07785 ( 9) link_ALPHA1-3 : bond 0.01049 ( 9) link_ALPHA1-3 : angle 1.82148 ( 27) hydrogen bonds : bond 0.03274 ( 604) hydrogen bonds : angle 4.84647 ( 1674) SS BOND : bond 0.00377 ( 36) SS BOND : angle 0.95299 ( 72) covalent geometry : bond 0.00271 (20622) covalent geometry : angle 0.58208 (28020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 352 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8342 (tp) cc_final: 0.8009 (tt) REVERT: B 154 MET cc_start: 0.8392 (mtt) cc_final: 0.8128 (mtt) REVERT: C 504 ARG cc_start: 0.6195 (tmt170) cc_final: 0.5941 (tmt170) REVERT: D 540 GLN cc_start: 0.8220 (tt0) cc_final: 0.7797 (tm-30) REVERT: D 625 ASN cc_start: 0.7661 (t0) cc_final: 0.7390 (t0) REVERT: E 530 MET cc_start: 0.6907 (tpt) cc_final: 0.6662 (tpt) REVERT: E 538 THR cc_start: 0.9240 (p) cc_final: 0.9004 (p) REVERT: E 596 TRP cc_start: 0.7454 (p90) cc_final: 0.6994 (p90) REVERT: E 623 TRP cc_start: 0.7780 (m100) cc_final: 0.7354 (m100) REVERT: F 589 ASP cc_start: 0.8183 (t0) cc_final: 0.7906 (t0) REVERT: F 632 ASP cc_start: 0.8495 (t0) cc_final: 0.8267 (t0) outliers start: 34 outliers final: 29 residues processed: 371 average time/residue: 0.3029 time to fit residues: 174.2583 Evaluate side-chains 361 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 180 optimal weight: 0.0970 chunk 139 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112329 restraints weight = 32801.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113111 restraints weight = 28794.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113687 restraints weight = 24790.307| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20745 Z= 0.146 Angle : 0.634 9.337 28353 Z= 0.306 Chirality : 0.045 0.356 3384 Planarity : 0.004 0.049 3456 Dihedral : 11.639 114.335 4413 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.55 % Allowed : 14.57 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2427 helix: 0.60 (0.29), residues: 384 sheet: -0.29 (0.21), residues: 645 loop : -2.30 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 610 HIS 0.005 0.001 HIS C 374 PHE 0.019 0.001 PHE B 317 TYR 0.017 0.001 TYR K 51 ARG 0.009 0.001 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 42) link_NAG-ASN : angle 2.68374 ( 126) link_ALPHA1-6 : bond 0.00646 ( 9) link_ALPHA1-6 : angle 1.61131 ( 27) link_BETA1-4 : bond 0.00524 ( 24) link_BETA1-4 : angle 1.63308 ( 72) link_ALPHA1-2 : bond 0.00843 ( 3) link_ALPHA1-2 : angle 2.13745 ( 9) link_ALPHA1-3 : bond 0.00970 ( 9) link_ALPHA1-3 : angle 1.93810 ( 27) hydrogen bonds : bond 0.03311 ( 604) hydrogen bonds : angle 4.68766 ( 1674) SS BOND : bond 0.00372 ( 36) SS BOND : angle 0.92858 ( 72) covalent geometry : bond 0.00343 (20622) covalent geometry : angle 0.59771 (28020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 2.190 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 84 LEU cc_start: 0.8356 (tp) cc_final: 0.8016 (tt) REVERT: B 154 MET cc_start: 0.8426 (mtt) cc_final: 0.8199 (mtt) REVERT: C 342 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6507 (tt) REVERT: D 540 GLN cc_start: 0.8210 (tt0) cc_final: 0.7833 (tm-30) REVERT: D 625 ASN cc_start: 0.7770 (t0) cc_final: 0.7464 (t0) REVERT: E 596 TRP cc_start: 0.7510 (p90) cc_final: 0.6987 (p90) REVERT: F 589 ASP cc_start: 0.8272 (t0) cc_final: 0.8006 (t0) REVERT: F 617 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7221 (ttp-170) REVERT: F 632 ASP cc_start: 0.8526 (t0) cc_final: 0.8269 (t0) REVERT: I 12 LYS cc_start: 0.8365 (mmmm) cc_final: 0.7948 (mmmm) REVERT: L 38 TYR cc_start: 0.7971 (m-80) cc_final: 0.7710 (m-10) outliers start: 54 outliers final: 42 residues processed: 370 average time/residue: 0.2953 time to fit residues: 170.6360 Evaluate side-chains 373 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 329 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 187 optimal weight: 4.9990 chunk 47 optimal weight: 0.0370 chunk 212 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS C 66 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109478 restraints weight = 33117.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110030 restraints weight = 30420.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110462 restraints weight = 28013.872| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20745 Z= 0.183 Angle : 0.667 9.365 28353 Z= 0.323 Chirality : 0.046 0.351 3384 Planarity : 0.004 0.051 3456 Dihedral : 11.356 115.497 4413 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.68 % Allowed : 15.89 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2427 helix: 0.65 (0.29), residues: 387 sheet: -0.26 (0.21), residues: 645 loop : -2.30 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 571 HIS 0.006 0.001 HIS C 374 PHE 0.014 0.002 PHE A 317 TYR 0.017 0.001 TYR K 51 ARG 0.008 0.000 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 42) link_NAG-ASN : angle 2.83444 ( 126) link_ALPHA1-6 : bond 0.00622 ( 9) link_ALPHA1-6 : angle 1.60164 ( 27) link_BETA1-4 : bond 0.00534 ( 24) link_BETA1-4 : angle 1.60501 ( 72) link_ALPHA1-2 : bond 0.00745 ( 3) link_ALPHA1-2 : angle 2.11825 ( 9) link_ALPHA1-3 : bond 0.00980 ( 9) link_ALPHA1-3 : angle 1.97740 ( 27) hydrogen bonds : bond 0.03509 ( 604) hydrogen bonds : angle 4.71018 ( 1674) SS BOND : bond 0.00475 ( 36) SS BOND : angle 1.14253 ( 72) covalent geometry : bond 0.00434 (20622) covalent geometry : angle 0.62963 (28020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 349 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8433 (tp) cc_final: 0.8080 (tt) REVERT: A 425 ASN cc_start: 0.7859 (t0) cc_final: 0.7541 (t0) REVERT: B 99 ASP cc_start: 0.7372 (t70) cc_final: 0.6853 (t0) REVERT: B 100 MET cc_start: 0.8721 (mtp) cc_final: 0.8520 (mtm) REVERT: C 342 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7042 (tt) REVERT: D 538 THR cc_start: 0.9132 (p) cc_final: 0.8856 (t) REVERT: D 625 ASN cc_start: 0.7708 (t0) cc_final: 0.7391 (t0) REVERT: F 589 ASP cc_start: 0.8255 (t0) cc_final: 0.7995 (t0) REVERT: F 632 ASP cc_start: 0.8562 (t0) cc_final: 0.8326 (t0) REVERT: I 12 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8123 (mmmm) outliers start: 78 outliers final: 59 residues processed: 398 average time/residue: 0.2860 time to fit residues: 179.9892 Evaluate side-chains 390 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 330 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 106 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.106317 restraints weight = 33145.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.106944 restraints weight = 30283.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107304 restraints weight = 28491.399| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20745 Z= 0.231 Angle : 0.736 9.557 28353 Z= 0.359 Chirality : 0.048 0.361 3384 Planarity : 0.004 0.080 3456 Dihedral : 11.291 115.539 4413 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.68 % Favored : 90.28 % Rotamer: Outliers : 4.01 % Allowed : 17.11 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2427 helix: 0.64 (0.29), residues: 384 sheet: -0.19 (0.21), residues: 618 loop : -2.36 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 571 HIS 0.007 0.002 HIS C 374 PHE 0.021 0.002 PHE H 29 TYR 0.018 0.002 TYR A 191 ARG 0.007 0.001 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 42) link_NAG-ASN : angle 3.07428 ( 126) link_ALPHA1-6 : bond 0.00593 ( 9) link_ALPHA1-6 : angle 1.54917 ( 27) link_BETA1-4 : bond 0.00587 ( 24) link_BETA1-4 : angle 1.76921 ( 72) link_ALPHA1-2 : bond 0.00537 ( 3) link_ALPHA1-2 : angle 2.27526 ( 9) link_ALPHA1-3 : bond 0.00925 ( 9) link_ALPHA1-3 : angle 2.07057 ( 27) hydrogen bonds : bond 0.03948 ( 604) hydrogen bonds : angle 4.87357 ( 1674) SS BOND : bond 0.00458 ( 36) SS BOND : angle 1.25231 ( 72) covalent geometry : bond 0.00550 (20622) covalent geometry : angle 0.69632 (28020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 334 time to evaluate : 2.228 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 84 LEU cc_start: 0.8473 (tp) cc_final: 0.8114 (tt) REVERT: B 99 ASP cc_start: 0.7510 (t70) cc_final: 0.6969 (t0) REVERT: C 104 MET cc_start: 0.8650 (tpp) cc_final: 0.8425 (tpt) REVERT: C 180 ASP cc_start: 0.8794 (m-30) cc_final: 0.8314 (m-30) REVERT: C 504 ARG cc_start: 0.5974 (tmt170) cc_final: 0.5763 (tmm160) REVERT: D 522 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: D 538 THR cc_start: 0.9142 (p) cc_final: 0.8908 (t) REVERT: F 589 ASP cc_start: 0.8359 (t0) cc_final: 0.8033 (t0) REVERT: G 119 GLN cc_start: 0.8246 (pm20) cc_final: 0.7865 (pm20) REVERT: H 78 THR cc_start: 0.8184 (m) cc_final: 0.7822 (p) REVERT: I 12 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8316 (mmmm) REVERT: L 68 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7954 (ttpt) outliers start: 85 outliers final: 68 residues processed: 389 average time/residue: 0.2918 time to fit residues: 179.5858 Evaluate side-chains 389 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 320 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 236 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108905 restraints weight = 32574.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109261 restraints weight = 29038.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110118 restraints weight = 28191.492| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 20745 Z= 0.151 Angle : 0.667 9.261 28353 Z= 0.323 Chirality : 0.046 0.349 3384 Planarity : 0.004 0.058 3456 Dihedral : 10.620 111.340 4413 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.30 % Allowed : 18.95 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2427 helix: 0.79 (0.29), residues: 384 sheet: -0.38 (0.21), residues: 654 loop : -2.30 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 571 HIS 0.005 0.001 HIS C 330 PHE 0.019 0.001 PHE H 29 TYR 0.018 0.001 TYR B 435 ARG 0.005 0.000 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 42) link_NAG-ASN : angle 2.81779 ( 126) link_ALPHA1-6 : bond 0.00773 ( 9) link_ALPHA1-6 : angle 1.39355 ( 27) link_BETA1-4 : bond 0.00536 ( 24) link_BETA1-4 : angle 1.65311 ( 72) link_ALPHA1-2 : bond 0.00975 ( 3) link_ALPHA1-2 : angle 2.43918 ( 9) link_ALPHA1-3 : bond 0.00973 ( 9) link_ALPHA1-3 : angle 1.88810 ( 27) hydrogen bonds : bond 0.03361 ( 604) hydrogen bonds : angle 4.66800 ( 1674) SS BOND : bond 0.00459 ( 36) SS BOND : angle 1.14321 ( 72) covalent geometry : bond 0.00356 (20622) covalent geometry : angle 0.62959 (28020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 346 time to evaluate : 2.376 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 84 LEU cc_start: 0.8481 (tp) cc_final: 0.8108 (tt) REVERT: B 42 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8157 (m) REVERT: B 99 ASP cc_start: 0.7447 (t70) cc_final: 0.6919 (t0) REVERT: C 104 MET cc_start: 0.8605 (tpp) cc_final: 0.8402 (tpt) REVERT: C 342 LEU cc_start: 0.7196 (tt) cc_final: 0.6584 (tt) REVERT: D 538 THR cc_start: 0.9161 (p) cc_final: 0.8902 (t) REVERT: D 596 TRP cc_start: 0.7986 (p90) cc_final: 0.7626 (p90) REVERT: E 612 SER cc_start: 0.7974 (m) cc_final: 0.7626 (t) REVERT: F 589 ASP cc_start: 0.8270 (t0) cc_final: 0.7932 (t0) REVERT: H 78 THR cc_start: 0.8132 (m) cc_final: 0.7760 (p) REVERT: I 12 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8307 (mmmm) REVERT: L 68 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8006 (ttpt) outliers start: 70 outliers final: 62 residues processed: 388 average time/residue: 0.2951 time to fit residues: 179.7204 Evaluate side-chains 395 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 332 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 522 PHE Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 188 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 374 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104308 restraints weight = 33177.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.104617 restraints weight = 30154.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105395 restraints weight = 26343.557| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 20745 Z= 0.252 Angle : 0.764 9.544 28353 Z= 0.372 Chirality : 0.049 0.359 3384 Planarity : 0.004 0.058 3456 Dihedral : 10.786 114.360 4413 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.22 % Favored : 89.70 % Rotamer: Outliers : 4.43 % Allowed : 17.92 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.17), residues: 2427 helix: 0.67 (0.29), residues: 384 sheet: -0.25 (0.21), residues: 627 loop : -2.37 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 571 HIS 0.008 0.002 HIS C 374 PHE 0.022 0.002 PHE H 29 TYR 0.019 0.002 TYR K 51 ARG 0.005 0.001 ARG B 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 42) link_NAG-ASN : angle 3.14969 ( 126) link_ALPHA1-6 : bond 0.00624 ( 9) link_ALPHA1-6 : angle 1.53747 ( 27) link_BETA1-4 : bond 0.00613 ( 24) link_BETA1-4 : angle 1.82238 ( 72) link_ALPHA1-2 : bond 0.00538 ( 3) link_ALPHA1-2 : angle 2.65970 ( 9) link_ALPHA1-3 : bond 0.00889 ( 9) link_ALPHA1-3 : angle 2.03307 ( 27) hydrogen bonds : bond 0.04057 ( 604) hydrogen bonds : angle 4.95542 ( 1674) SS BOND : bond 0.00542 ( 36) SS BOND : angle 1.35250 ( 72) covalent geometry : bond 0.00599 (20622) covalent geometry : angle 0.72378 (28020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 334 time to evaluate : 2.103 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 84 LEU cc_start: 0.8565 (tp) cc_final: 0.8186 (tt) REVERT: A 217 TYR cc_start: 0.8811 (m-80) cc_final: 0.8508 (m-80) REVERT: B 99 ASP cc_start: 0.7618 (t70) cc_final: 0.7071 (t0) REVERT: D 522 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5255 (m-80) REVERT: D 538 THR cc_start: 0.9194 (p) cc_final: 0.8970 (t) REVERT: E 612 SER cc_start: 0.8280 (m) cc_final: 0.7923 (t) REVERT: F 589 ASP cc_start: 0.8345 (t0) cc_final: 0.7988 (t0) REVERT: G 119 GLN cc_start: 0.8420 (pm20) cc_final: 0.8046 (pm20) REVERT: I 12 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8527 (mmmm) REVERT: K 63 ARG cc_start: 0.7461 (mtp-110) cc_final: 0.7111 (mtp180) outliers start: 94 outliers final: 72 residues processed: 395 average time/residue: 0.2862 time to fit residues: 178.5410 Evaluate side-chains 401 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 328 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 522 PHE Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 124 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107176 restraints weight = 32542.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107502 restraints weight = 28863.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108247 restraints weight = 26819.625| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20745 Z= 0.168 Angle : 0.699 9.215 28353 Z= 0.337 Chirality : 0.046 0.345 3384 Planarity : 0.004 0.052 3456 Dihedral : 10.128 109.837 4413 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.57 % Favored : 91.35 % Rotamer: Outliers : 3.77 % Allowed : 19.05 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.83 (0.17), residues: 2427 helix: 0.76 (0.29), residues: 384 sheet: -0.35 (0.21), residues: 642 loop : -2.33 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP F 571 HIS 0.005 0.001 HIS C 330 PHE 0.021 0.002 PHE H 29 TYR 0.018 0.001 TYR K 51 ARG 0.005 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 42) link_NAG-ASN : angle 2.91881 ( 126) link_ALPHA1-6 : bond 0.00772 ( 9) link_ALPHA1-6 : angle 1.31999 ( 27) link_BETA1-4 : bond 0.00564 ( 24) link_BETA1-4 : angle 1.70823 ( 72) link_ALPHA1-2 : bond 0.01128 ( 3) link_ALPHA1-2 : angle 2.69765 ( 9) link_ALPHA1-3 : bond 0.00947 ( 9) link_ALPHA1-3 : angle 1.78913 ( 27) hydrogen bonds : bond 0.03482 ( 604) hydrogen bonds : angle 4.75180 ( 1674) SS BOND : bond 0.00464 ( 36) SS BOND : angle 1.19567 ( 72) covalent geometry : bond 0.00399 (20622) covalent geometry : angle 0.66124 (28020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 332 time to evaluate : 2.241 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 84 LEU cc_start: 0.8532 (tp) cc_final: 0.8158 (tt) REVERT: A 217 TYR cc_start: 0.8754 (m-80) cc_final: 0.8539 (m-80) REVERT: B 99 ASP cc_start: 0.7484 (t70) cc_final: 0.6955 (t0) REVERT: C 33 ASN cc_start: 0.7010 (m-40) cc_final: 0.6790 (m-40) REVERT: C 342 LEU cc_start: 0.7177 (tt) cc_final: 0.6478 (tt) REVERT: D 538 THR cc_start: 0.9146 (p) cc_final: 0.8902 (t) REVERT: D 596 TRP cc_start: 0.7990 (p90) cc_final: 0.7581 (p90) REVERT: E 530 MET cc_start: 0.7251 (tpt) cc_final: 0.7049 (tpt) REVERT: G 119 GLN cc_start: 0.8394 (pm20) cc_final: 0.8035 (pm20) REVERT: H 73 ASP cc_start: 0.7686 (t0) cc_final: 0.7281 (m-30) REVERT: I 12 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8510 (mmmm) REVERT: K 63 ARG cc_start: 0.7339 (mtp-110) cc_final: 0.7065 (mtp180) outliers start: 80 outliers final: 65 residues processed: 386 average time/residue: 0.2841 time to fit residues: 172.8772 Evaluate side-chains 396 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 331 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 522 PHE Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 199 optimal weight: 6.9990 chunk 123 optimal weight: 0.3980 chunk 193 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107871 restraints weight = 32690.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108198 restraints weight = 28942.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109043 restraints weight = 28652.325| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20745 Z= 0.161 Angle : 0.688 9.028 28353 Z= 0.332 Chirality : 0.046 0.346 3384 Planarity : 0.004 0.050 3456 Dihedral : 9.681 108.369 4413 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.06 % Favored : 90.89 % Rotamer: Outliers : 3.25 % Allowed : 19.42 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2427 helix: 0.85 (0.29), residues: 384 sheet: -0.36 (0.21), residues: 645 loop : -2.30 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 571 HIS 0.005 0.001 HIS C 330 PHE 0.021 0.002 PHE H 29 TYR 0.018 0.001 TYR K 51 ARG 0.004 0.000 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 42) link_NAG-ASN : angle 2.84027 ( 126) link_ALPHA1-6 : bond 0.00781 ( 9) link_ALPHA1-6 : angle 1.32472 ( 27) link_BETA1-4 : bond 0.00571 ( 24) link_BETA1-4 : angle 1.63515 ( 72) link_ALPHA1-2 : bond 0.01239 ( 3) link_ALPHA1-2 : angle 2.79609 ( 9) link_ALPHA1-3 : bond 0.00904 ( 9) link_ALPHA1-3 : angle 1.70619 ( 27) hydrogen bonds : bond 0.03363 ( 604) hydrogen bonds : angle 4.67173 ( 1674) SS BOND : bond 0.00516 ( 36) SS BOND : angle 1.29442 ( 72) covalent geometry : bond 0.00382 (20622) covalent geometry : angle 0.65187 (28020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 340 time to evaluate : 2.180 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 84 LEU cc_start: 0.8503 (tp) cc_final: 0.8123 (tt) REVERT: A 360 LYS cc_start: 0.7445 (ttmm) cc_final: 0.7190 (mtpp) REVERT: B 99 ASP cc_start: 0.7467 (t70) cc_final: 0.6954 (t0) REVERT: C 342 LEU cc_start: 0.7212 (tt) cc_final: 0.6531 (tt) REVERT: D 538 THR cc_start: 0.9122 (p) cc_final: 0.8894 (t) REVERT: D 596 TRP cc_start: 0.7964 (p90) cc_final: 0.7543 (p90) REVERT: F 589 ASP cc_start: 0.8208 (t0) cc_final: 0.7863 (t0) REVERT: G 119 GLN cc_start: 0.8394 (pm20) cc_final: 0.8074 (pm20) REVERT: H 73 ASP cc_start: 0.7759 (t0) cc_final: 0.7339 (m-30) REVERT: I 12 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8527 (mmmm) REVERT: K 63 ARG cc_start: 0.7438 (mtp-110) cc_final: 0.7115 (mtp180) REVERT: L 41 HIS cc_start: 0.8492 (m-70) cc_final: 0.8266 (m-70) outliers start: 69 outliers final: 67 residues processed: 385 average time/residue: 0.2847 time to fit residues: 172.1442 Evaluate side-chains 402 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 522 PHE Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 0.0010 chunk 76 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 160 optimal weight: 0.3980 chunk 203 optimal weight: 1.9990 chunk 236 optimal weight: 0.0070 chunk 178 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111674 restraints weight = 32632.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112240 restraints weight = 27306.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112718 restraints weight = 25201.706| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20745 Z= 0.116 Angle : 0.646 9.160 28353 Z= 0.311 Chirality : 0.045 0.325 3384 Planarity : 0.003 0.047 3456 Dihedral : 8.956 102.050 4413 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.50 % Allowed : 20.51 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2427 helix: 1.31 (0.29), residues: 366 sheet: -0.13 (0.22), residues: 603 loop : -2.14 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 571 HIS 0.004 0.001 HIS B 374 PHE 0.019 0.001 PHE H 29 TYR 0.015 0.001 TYR K 51 ARG 0.005 0.000 ARG I 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 42) link_NAG-ASN : angle 2.52288 ( 126) link_ALPHA1-6 : bond 0.00928 ( 9) link_ALPHA1-6 : angle 1.23012 ( 27) link_BETA1-4 : bond 0.00549 ( 24) link_BETA1-4 : angle 1.45939 ( 72) link_ALPHA1-2 : bond 0.01685 ( 3) link_ALPHA1-2 : angle 2.68642 ( 9) link_ALPHA1-3 : bond 0.00888 ( 9) link_ALPHA1-3 : angle 1.51905 ( 27) hydrogen bonds : bond 0.02812 ( 604) hydrogen bonds : angle 4.45305 ( 1674) SS BOND : bond 0.00472 ( 36) SS BOND : angle 1.17818 ( 72) covalent geometry : bond 0.00267 (20622) covalent geometry : angle 0.61512 (28020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5833.00 seconds wall clock time: 104 minutes 33.48 seconds (6273.48 seconds total)