Starting phenix.real_space_refine on Thu Aug 6 20:59:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9py5_72009/08_2026/9py5_72009.cif Found real_map, /net/cci-nas-00/data/ceres_data/9py5_72009/08_2026/9py5_72009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9py5_72009/08_2026/9py5_72009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9py5_72009/08_2026/9py5_72009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9py5_72009/08_2026/9py5_72009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9py5_72009/08_2026/9py5_72009.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 103 5.16 5 C 10468 2.51 5 N 2786 2.21 5 O 3349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16706 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4619 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 23, 'TRANS': 559} Chain breaks: 4 Chain: "B" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4582 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 23, 'TRANS': 553} Chain breaks: 4 Chain: "C" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4558 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 23, 'TRANS': 550} Chain breaks: 4 Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" 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: "J" 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: "K" 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: "M" 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: "N" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" 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: "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: 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" 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: "X" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 3.50, per 1000 atoms: 0.21 Number of scatterers: 16706 At special positions: 0 Unit cell: (122, 134.407, 150.949, 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 103 16.00 O 3349 8.00 N 2786 7.00 C 10468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.09 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 662 " distance=2.02 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS C 501 " distance=2.02 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 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=2.03 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 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 445 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA N 3 " - " MAN N 7 " " MAN N 4 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 6 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " BETA1-6 " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 701 " - " ASN A 88 " " NAG A 702 " - " ASN A 133 " " NAG A 703 " - " ASN A 234 " " NAG A 704 " - " ASN A 241 " " NAG A 705 " - " ASN A 269 " " NAG A 706 " - " ASN A 301 " " NAG A 707 " - " ASN A 339 " " NAG A 708 " - " ASN A 363 " " NAG A 709 " - " ASN A 392 " " NAG A 710 " - " ASN A 448 " " NAG A 711 " - " ASN A 465 " " NAG B 701 " - " ASN B 133 " " NAG B 702 " - " ASN B 197 " " NAG B 703 " - " ASN B 234 " " NAG B 704 " - " ASN B 241 " " NAG B 705 " - " ASN B 269 " " NAG B 706 " - " ASN B 276 " " NAG B 707 " - " ASN B 301 " " NAG B 708 " - " ASN B 339 " " NAG B 709 " - " ASN B 363 " " NAG B 710 " - " ASN B 392 " " NAG B 711 " - " ASN B 448 " " NAG B 712 " - " ASN B 465 " " NAG C 701 " - " ASN C 133 " " NAG C 702 " - " ASN C 241 " " NAG C 703 " - " ASN C 269 " " NAG C 704 " - " ASN C 276 " " NAG C 705 " - " ASN C 339 " " NAG C 706 " - " ASN C 363 " " NAG C 707 " - " ASN C 386 " " NAG C 708 " - " ASN C 392 " " NAG C 709 " - " ASN C 448 " " NAG C 710 " - " ASN C 465 " " NAG D 1 " - " ASN A 156 " " NAG E 1 " - " ASN A 160 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 276 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN B 156 " " NAG N 1 " - " ASN B 160 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 332 " " NAG Q 1 " - " ASN B 386 " " NAG R 1 " - " ASN C 156 " " NAG S 1 " - " ASN C 160 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 234 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 332 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 535.2 milliseconds 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 33 sheets defined 24.7% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.501A pdb=" N ALA A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.756A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.014A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG 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 474 through 483 removed outlier: 3.888A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.900A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.533A pdb=" N THR A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 534' Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.738A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 597 removed outlier: 3.917A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.894A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.520A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.953A pdb=" N TYR B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.014A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.367A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.180A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.767A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.570A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.306A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.660A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG 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 474 through 483 removed outlier: 3.550A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.322A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.560A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.668A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.752A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU C 648 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN C 650 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.701A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.604A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.526A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.887A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 293 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 334 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 333 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.703A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 309 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.121A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.183A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 75 through 76 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 129 through 130 Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.124A pdb=" N TYR H 98 " --> pdb=" O TYR H 100F" (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.871A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 259 through 261 removed outlier: 10.171A pdb=" N LYS B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE B 294 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLU B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N VAL B 292 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN B 448 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLN B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 293 " --> pdb=" O THR B 334 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 334 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 7.027A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLN B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN B 448 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N VAL B 292 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLU B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE B 294 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N LYS B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 301 through 312 removed outlier: 6.831A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.294A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.518A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.925A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.688A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'C' and resid 200 through 203 removed outlier: 4.375A pdb=" N ALA C 433 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 261 removed outlier: 9.635A pdb=" N GLU C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N VAL C 292 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR C 293 " --> pdb=" O THR C 334 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR C 334 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.366A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N VAL C 292 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N GLU C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.030A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.635A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE H 102 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.635A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.508A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 619 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.79 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: 5228 1.35 - 1.49: 4598 1.49 - 1.63: 7077 1.63 - 1.76: 3 1.76 - 1.90: 131 Bond restraints: 17037 Sorted by residual: bond pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " ideal model delta sigma weight residual 1.808 1.898 -0.090 3.30e-02 9.18e+02 7.50e+00 bond pdb=" C THR A 415 " pdb=" N LEU A 416 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.59e-02 3.96e+03 4.65e+00 bond pdb=" CA ASP C 150 " pdb=" CB ASP C 150 " ideal model delta sigma weight residual 1.527 1.572 -0.044 2.48e-02 1.63e+03 3.19e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" CB VAL B 496 " pdb=" CG1 VAL B 496 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 17032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22386 2.55 - 5.09: 663 5.09 - 7.64: 77 7.64 - 10.19: 11 10.19 - 12.74: 2 Bond angle restraints: 23139 Sorted by residual: angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 123.70 -9.30 2.30e+00 1.89e-01 1.64e+01 angle pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " pdb=" C5 NAG K 1 " ideal model delta sigma weight residual 113.21 125.21 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N PHE A 376 " pdb=" CA PHE A 376 " pdb=" CB PHE A 376 " ideal model delta sigma weight residual 111.20 117.52 -6.32 1.62e+00 3.81e-01 1.52e+01 angle pdb=" N HIS L 93 " pdb=" CA HIS L 93 " pdb=" C HIS L 93 " ideal model delta sigma weight residual 109.80 103.30 6.50 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA PHE A 376 " pdb=" CB PHE A 376 " pdb=" CG PHE A 376 " ideal model delta sigma weight residual 113.80 117.56 -3.76 1.00e+00 1.00e+00 1.41e+01 ... (remaining 23134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 10603 25.96 - 51.92: 580 51.92 - 77.88: 101 77.88 - 103.84: 23 103.84 - 129.80: 9 Dihedral angle restraints: 11316 sinusoidal: 5646 harmonic: 5670 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual -86.00 -157.07 71.07 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual 93.00 155.98 -62.98 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 385 " pdb=" CB CYS A 385 " ideal model delta sinusoidal sigma weight residual -86.00 -28.63 -57.37 1 1.00e+01 1.00e-02 4.42e+01 ... (remaining 11313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2395 0.068 - 0.137: 383 0.137 - 0.205: 60 0.205 - 0.273: 7 0.273 - 0.342: 3 Chirality restraints: 2848 Sorted by residual: chirality pdb=" C1 NAG B 712 " pdb=" ND2 ASN B 465 " pdb=" C2 NAG B 712 " pdb=" O5 NAG B 712 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C1 NAG B 706 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 706 " pdb=" O5 NAG B 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CG LEU A 416 " pdb=" CB LEU A 416 " pdb=" CD1 LEU A 416 " pdb=" CD2 LEU A 416 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2845 not shown) Planarity restraints: 2878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " -0.339 9.50e-02 1.11e+02 1.53e-01 1.84e+01 pdb=" NE ARG A 192 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 237 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C GLY C 237 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY C 237 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 238 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 54 " 0.209 9.50e-02 1.11e+02 9.42e-02 6.58e+00 pdb=" NE ARG L 54 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG L 54 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG L 54 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG L 54 " 0.001 2.00e-02 2.50e+03 ... (remaining 2875 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 518 2.70 - 3.25: 16226 3.25 - 3.80: 25670 3.80 - 4.35: 33194 4.35 - 4.90: 55346 Nonbonded interactions: 130954 Sorted by model distance: nonbonded pdb=" OG1 THR A 51 " pdb=" O HIS C 564 " model vdw 2.154 3.040 nonbonded pdb=" O THR A 278 " pdb=" NH2 ARG A 456 " model vdw 2.217 3.120 nonbonded pdb=" O PHE C 233 " pdb=" NH2 ARG C 273 " model vdw 2.222 3.120 nonbonded pdb=" O THR B 278 " pdb=" NH2 ARG B 456 " model vdw 2.239 3.120 nonbonded pdb=" ND2 ASN C 463 " pdb=" O ASN C 465 " model vdw 2.246 3.120 ... (remaining 130949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 58 or resid 65 through 403 or resid 414 through \ 520 or resid 522 through 546 or resid 564 through 662 or resid 702 through 711) \ ) selection = (chain 'B' and (resid 35 through 58 or resid 65 through 403 or resid 414 through \ 504 or resid 522 through 662 or resid 703 through 712)) selection = (chain 'C' and (resid 35 through 412 or resid 414 through 504 or resid 522 throu \ gh 546 or resid 564 through 710)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'V' } 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.250 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 0.090 17159 Z= 0.228 Angle : 1.061 19.897 23467 Z= 0.508 Chirality : 0.053 0.342 2848 Planarity : 0.006 0.153 2826 Dihedral : 15.954 129.803 7546 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.81 % Allowed : 16.87 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 1929 helix: 0.77 (0.25), residues: 386 sheet: 0.15 (0.23), residues: 499 loop : -0.54 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG A 192 TYR 0.034 0.002 TYR L 91 PHE 0.028 0.003 PHE A 376 TRP 0.025 0.002 TRP B 631 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (17037) covalent geometry : angle 0.99923 / 0.49 (23139) SS BOND : bond 0.01270 / 0.79 ( 38) SS BOND : angle 4.00629 / 2.82 ( 76) hydrogen bonds : bond 0.12878 / 8.54 ( 598) hydrogen bonds : angle 7.29911 / 5.05 ( 1659) link_ALPHA1-3 : bond 0.01160 / 0.56 ( 5) link_ALPHA1-3 : angle 3.61791 / 2.92 ( 15) link_ALPHA1-6 : bond 0.01305 / 0.65 ( 3) link_ALPHA1-6 : angle 2.87146 / 1.91 ( 9) link_BETA1-4 : bond 0.00862 / 0.44 ( 23) link_BETA1-4 : angle 3.03083 / 1.85 ( 69) link_BETA1-6 : bond 0.02098 / 1.10 ( 1) link_BETA1-6 : angle 0.96399 / 0.54 ( 3) link_NAG-ASN : bond 0.00471 / 0.32 ( 52) link_NAG-ASN : angle 2.75208 / 1.84 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 260 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7213 (tmtt) REVERT: A 161 MET cc_start: 0.8043 (tpp) cc_final: 0.7603 (ttm) REVERT: A 377 ASN cc_start: 0.8115 (t0) cc_final: 0.7755 (p0) REVERT: B 151 ARG cc_start: 0.7408 (ttt180) cc_final: 0.6582 (tpm170) REVERT: B 202 THR cc_start: 0.9044 (m) cc_final: 0.8744 (p) REVERT: B 434 MET cc_start: 0.8072 (ttp) cc_final: 0.7853 (ttp) REVERT: C 104 MET cc_start: 0.8758 (ttt) cc_final: 0.8454 (ttt) REVERT: C 426 MET cc_start: 0.7990 (tpp) cc_final: 0.7661 (tpt) REVERT: C 475 MET cc_start: 0.7843 (mmm) cc_final: 0.7598 (mmt) REVERT: C 565 LEU cc_start: 0.8240 (mt) cc_final: 0.7992 (pt) REVERT: C 610 TRP cc_start: 0.7566 (t-100) cc_final: 0.7122 (t-100) REVERT: H 100 TYR cc_start: 0.8325 (m-80) cc_final: 0.7955 (m-10) REVERT: L 45 ARG cc_start: 0.8490 (ttm170) cc_final: 0.8257 (mtm110) REVERT: L 61 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8059 (ptt-90) outliers start: 14 outliers final: 6 residues processed: 271 average time/residue: 0.1257 time to fit residues: 51.5236 Evaluate side-chains 192 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain L residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN A 656 ASN B 130 HIS B 575 GLN B 656 ASN C 591 GLN C 630 GLN L 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093049 restraints weight = 35936.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.096346 restraints weight = 17671.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098487 restraints weight = 11548.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099906 restraints weight = 8853.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100665 restraints weight = 7415.277| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17159 Z= 0.202 Angle : 0.806 16.586 23467 Z= 0.375 Chirality : 0.048 0.359 2848 Planarity : 0.004 0.047 2826 Dihedral : 9.464 110.045 3865 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.05 % Allowed : 17.79 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 1929 helix: 1.09 (0.25), residues: 402 sheet: 0.37 (0.23), residues: 494 loop : -0.52 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 108 TYR 0.025 0.002 TYR L 91 PHE 0.029 0.002 PHE A 522 TRP 0.017 0.002 TRP H 34 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (17037) covalent geometry : angle 0.72326 / 0.35 (23139) SS BOND : bond 0.00931 / 0.67 ( 38) SS BOND : angle 3.21556 / 2.36 ( 76) hydrogen bonds : bond 0.04619 / 3.02 ( 598) hydrogen bonds : angle 6.07003 / 4.18 ( 1659) link_ALPHA1-3 : bond 0.01185 / 0.57 ( 5) link_ALPHA1-3 : angle 2.50431 / 2.02 ( 15) link_ALPHA1-6 : bond 0.02164 / 1.08 ( 3) link_ALPHA1-6 : angle 3.04415 / 2.23 ( 9) link_BETA1-4 : bond 0.00389 / 0.18 ( 23) link_BETA1-4 : angle 2.33620 / 1.52 ( 69) link_BETA1-6 : bond 0.00644 / 0.34 ( 1) link_BETA1-6 : angle 1.46933 / 0.82 ( 3) link_NAG-ASN : bond 0.00460 / 0.29 ( 52) link_NAG-ASN : angle 3.39710 / 2.23 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8487 (mmmt) cc_final: 0.7142 (tmtt) REVERT: A 377 ASN cc_start: 0.8027 (t0) cc_final: 0.7670 (p0) REVERT: A 502 LYS cc_start: 0.7724 (tttt) cc_final: 0.7472 (tttt) REVERT: A 530 MET cc_start: 0.8090 (ttm) cc_final: 0.7213 (mtp) REVERT: A 622 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7063 (pt) REVERT: B 151 ARG cc_start: 0.7482 (ttt180) cc_final: 0.6671 (tpm170) REVERT: B 323 ILE cc_start: 0.9102 (mp) cc_final: 0.8872 (tt) REVERT: B 564 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.5531 (t70) REVERT: L 17 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7709 (mt-10) REVERT: L 45 ARG cc_start: 0.8451 (ttm170) cc_final: 0.8183 (mtm110) outliers start: 53 outliers final: 33 residues processed: 235 average time/residue: 0.1201 time to fit residues: 43.0150 Evaluate side-chains 205 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain L residue 61 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 167 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 652 GLN C 563 GLN C 591 GLN H 54 HIS L 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.116228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093126 restraints weight = 37235.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096491 restraints weight = 18698.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098719 restraints weight = 12421.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100126 restraints weight = 9587.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101024 restraints weight = 8112.581| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17159 Z= 0.151 Angle : 0.720 15.936 23467 Z= 0.336 Chirality : 0.046 0.335 2848 Planarity : 0.004 0.048 2826 Dihedral : 8.641 103.709 3861 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.22 % Allowed : 18.71 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 1929 helix: 1.26 (0.25), residues: 410 sheet: 0.46 (0.23), residues: 493 loop : -0.49 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 108 TYR 0.019 0.001 TYR L 91 PHE 0.025 0.002 PHE A 522 TRP 0.017 0.001 TRP H 34 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (17037) covalent geometry : angle 0.64185 / 0.31 (23139) SS BOND : bond 0.00737 / 0.53 ( 38) SS BOND : angle 3.01929 / 2.21 ( 76) hydrogen bonds : bond 0.04170 / 2.74 ( 598) hydrogen bonds : angle 5.78684 / 3.98 ( 1659) link_ALPHA1-3 : bond 0.01149 / 0.55 ( 5) link_ALPHA1-3 : angle 2.42288 / 2.00 ( 15) link_ALPHA1-6 : bond 0.01929 / 0.97 ( 3) link_ALPHA1-6 : angle 3.19093 / 2.33 ( 9) link_BETA1-4 : bond 0.00398 / 0.20 ( 23) link_BETA1-4 : angle 2.02832 / 1.32 ( 69) link_BETA1-6 : bond 0.00691 / 0.36 ( 1) link_BETA1-6 : angle 1.47929 / 0.82 ( 3) link_NAG-ASN : bond 0.00476 / 0.31 ( 52) link_NAG-ASN : angle 3.06222 / 1.96 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8377 (mmmt) cc_final: 0.6984 (tmtt) REVERT: A 377 ASN cc_start: 0.8018 (t0) cc_final: 0.7607 (p0) REVERT: B 151 ARG cc_start: 0.7459 (ttt180) cc_final: 0.6649 (tpm170) REVERT: B 161 MET cc_start: 0.8233 (tpt) cc_final: 0.7650 (tpt) REVERT: B 564 HIS cc_start: 0.5995 (OUTLIER) cc_final: 0.5553 (t70) REVERT: C 637 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.6086 (t0) REVERT: C 655 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5142 (ptmt) REVERT: H 77 GLN cc_start: 0.7056 (pt0) cc_final: 0.6772 (pt0) REVERT: H 108 ARG cc_start: 0.7455 (ttm110) cc_final: 0.7096 (ttm-80) REVERT: L 17 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7696 (mt-10) REVERT: L 31 TYR cc_start: 0.7307 (m-80) cc_final: 0.6955 (m-10) REVERT: L 45 ARG cc_start: 0.8409 (ttm170) cc_final: 0.8147 (mtm110) outliers start: 56 outliers final: 39 residues processed: 226 average time/residue: 0.1313 time to fit residues: 45.7251 Evaluate side-chains 215 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 61 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 38 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 95 optimal weight: 0.0030 chunk 17 optimal weight: 1.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.115038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.092582 restraints weight = 36255.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095901 restraints weight = 17788.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098079 restraints weight = 11607.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099468 restraints weight = 8874.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100331 restraints weight = 7467.549| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17159 Z= 0.164 Angle : 0.703 15.971 23467 Z= 0.329 Chirality : 0.045 0.324 2848 Planarity : 0.004 0.047 2826 Dihedral : 8.342 101.193 3861 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.68 % Allowed : 19.23 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1929 helix: 1.38 (0.26), residues: 404 sheet: 0.44 (0.23), residues: 498 loop : -0.46 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 108 TYR 0.018 0.001 TYR B 435 PHE 0.026 0.002 PHE A 522 TRP 0.014 0.001 TRP A 35 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (17037) covalent geometry : angle 0.62643 / 0.31 (23139) SS BOND : bond 0.00968 / 0.74 ( 38) SS BOND : angle 3.03319 / 2.22 ( 76) hydrogen bonds : bond 0.04055 / 2.68 ( 598) hydrogen bonds : angle 5.63203 / 3.88 ( 1659) link_ALPHA1-3 : bond 0.01144 / 0.55 ( 5) link_ALPHA1-3 : angle 2.42243 / 1.98 ( 15) link_ALPHA1-6 : bond 0.02105 / 1.05 ( 3) link_ALPHA1-6 : angle 3.22414 / 2.34 ( 9) link_BETA1-4 : bond 0.00367 / 0.19 ( 23) link_BETA1-4 : angle 1.94573 / 1.26 ( 69) link_BETA1-6 : bond 0.00145 / 0.08 ( 1) link_BETA1-6 : angle 0.72729 / 0.43 ( 3) link_NAG-ASN : bond 0.00490 / 0.32 ( 52) link_NAG-ASN : angle 2.96407 / 1.90 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7000 (tmtt) REVERT: A 373 THR cc_start: 0.8334 (p) cc_final: 0.7893 (t) REVERT: A 377 ASN cc_start: 0.8097 (t0) cc_final: 0.7634 (p0) REVERT: B 151 ARG cc_start: 0.7488 (ttt180) cc_final: 0.6647 (tpm170) REVERT: B 564 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.5618 (t70) REVERT: C 426 MET cc_start: 0.8155 (tpp) cc_final: 0.7823 (tpt) REVERT: C 637 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.6252 (t0) REVERT: H 99 GLU cc_start: 0.8093 (tp30) cc_final: 0.7610 (mm-30) REVERT: H 108 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7151 (ttm-80) REVERT: L 17 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7754 (mt-10) REVERT: L 45 ARG cc_start: 0.8296 (ttm170) cc_final: 0.8018 (mtm110) REVERT: L 90 GLN cc_start: 0.7158 (pt0) cc_final: 0.6812 (pt0) outliers start: 64 outliers final: 45 residues processed: 227 average time/residue: 0.1376 time to fit residues: 47.5763 Evaluate side-chains 216 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 61 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.116772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095674 restraints weight = 36617.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098892 restraints weight = 17671.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101005 restraints weight = 11364.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.102383 restraints weight = 8577.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103196 restraints weight = 7137.070| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17159 Z= 0.164 Angle : 0.702 15.679 23467 Z= 0.329 Chirality : 0.045 0.311 2848 Planarity : 0.004 0.046 2826 Dihedral : 8.177 99.078 3861 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 4.09 % Allowed : 19.40 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1929 helix: 1.43 (0.26), residues: 404 sheet: 0.45 (0.23), residues: 510 loop : -0.47 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 337 TYR 0.029 0.001 TYR C 39 PHE 0.026 0.002 PHE A 522 TRP 0.012 0.001 TRP H 34 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (17037) covalent geometry : angle 0.62727 / 0.31 (23139) SS BOND : bond 0.00901 / 0.69 ( 38) SS BOND : angle 3.06443 / 2.22 ( 76) hydrogen bonds : bond 0.03999 / 2.66 ( 598) hydrogen bonds : angle 5.57798 / 3.85 ( 1659) link_ALPHA1-3 : bond 0.01101 / 0.53 ( 5) link_ALPHA1-3 : angle 2.40859 / 1.97 ( 15) link_ALPHA1-6 : bond 0.02034 / 1.02 ( 3) link_ALPHA1-6 : angle 3.29676 / 2.39 ( 9) link_BETA1-4 : bond 0.00374 / 0.20 ( 23) link_BETA1-4 : angle 1.86374 / 1.21 ( 69) link_BETA1-6 : bond 0.00232 / 0.12 ( 1) link_BETA1-6 : angle 0.77591 / 0.46 ( 3) link_NAG-ASN : bond 0.00473 / 0.31 ( 52) link_NAG-ASN : angle 2.89988 / 1.86 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7032 (tmtt) REVERT: A 259 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8255 (mp) REVERT: A 373 THR cc_start: 0.8397 (p) cc_final: 0.7947 (t) REVERT: A 377 ASN cc_start: 0.8038 (t0) cc_final: 0.7463 (p0) REVERT: B 151 ARG cc_start: 0.7460 (ttt180) cc_final: 0.6665 (tpm170) REVERT: B 564 HIS cc_start: 0.6026 (OUTLIER) cc_final: 0.5469 (t70) REVERT: C 426 MET cc_start: 0.8179 (tpp) cc_final: 0.7846 (tpt) REVERT: C 637 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.6146 (t0) REVERT: H 99 GLU cc_start: 0.8076 (tp30) cc_final: 0.7584 (mm-30) REVERT: L 4 MET cc_start: 0.8414 (mmt) cc_final: 0.8058 (mmm) REVERT: L 17 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7860 (mt-10) REVERT: L 45 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7937 (mtm110) REVERT: L 61 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8226 (ptt-90) outliers start: 71 outliers final: 53 residues processed: 226 average time/residue: 0.1328 time to fit residues: 46.3916 Evaluate side-chains 223 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 22 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS L 27 GLN L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.114053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.091472 restraints weight = 36071.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.094746 restraints weight = 17813.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096882 restraints weight = 11672.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098284 restraints weight = 8964.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099172 restraints weight = 7541.948| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17159 Z= 0.174 Angle : 0.703 15.851 23467 Z= 0.329 Chirality : 0.045 0.325 2848 Planarity : 0.004 0.046 2826 Dihedral : 8.120 97.959 3861 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 4.61 % Allowed : 19.86 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1929 helix: 1.50 (0.26), residues: 398 sheet: 0.45 (0.23), residues: 510 loop : -0.47 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 337 TYR 0.019 0.001 TYR L 91 PHE 0.027 0.002 PHE A 522 TRP 0.016 0.001 TRP B 631 HIS 0.004 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17037) covalent geometry : angle 0.62960 / 0.31 (23139) SS BOND : bond 0.00834 / 0.63 ( 38) SS BOND : angle 3.06414 / 2.23 ( 76) hydrogen bonds : bond 0.03975 / 2.65 ( 598) hydrogen bonds : angle 5.53697 / 3.82 ( 1659) link_ALPHA1-3 : bond 0.01085 / 0.52 ( 5) link_ALPHA1-3 : angle 2.38564 / 1.93 ( 15) link_ALPHA1-6 : bond 0.01982 / 0.99 ( 3) link_ALPHA1-6 : angle 3.32199 / 2.39 ( 9) link_BETA1-4 : bond 0.00363 / 0.19 ( 23) link_BETA1-4 : angle 1.83570 / 1.20 ( 69) link_BETA1-6 : bond 0.00246 / 0.13 ( 1) link_BETA1-6 : angle 0.97786 / 0.57 ( 3) link_NAG-ASN : bond 0.00494 / 0.32 ( 52) link_NAG-ASN : angle 2.87946 / 1.85 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7129 (tmtt) REVERT: A 259 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 373 THR cc_start: 0.8444 (p) cc_final: 0.8005 (t) REVERT: A 452 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7978 (mt) REVERT: B 151 ARG cc_start: 0.7413 (ttt180) cc_final: 0.6608 (tpm170) REVERT: B 564 HIS cc_start: 0.6042 (OUTLIER) cc_final: 0.5357 (t70) REVERT: B 624 ASN cc_start: 0.7959 (t0) cc_final: 0.7721 (t0) REVERT: C 426 MET cc_start: 0.8199 (tpp) cc_final: 0.7870 (tpt) REVERT: C 624 ASN cc_start: 0.8766 (t0) cc_final: 0.8072 (t0) REVERT: C 637 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.6270 (t0) REVERT: H 99 GLU cc_start: 0.8119 (tp30) cc_final: 0.7644 (mm-30) REVERT: L 17 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7868 (mt-10) REVERT: L 31 TYR cc_start: 0.7710 (m-80) cc_final: 0.7455 (m-10) REVERT: L 45 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7952 (mtm110) REVERT: L 61 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8248 (ptt-90) outliers start: 80 outliers final: 58 residues processed: 230 average time/residue: 0.1206 time to fit residues: 43.4319 Evaluate side-chains 229 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 12 optimal weight: 4.9990 chunk 118 optimal weight: 0.2980 chunk 183 optimal weight: 0.6980 chunk 95 optimal weight: 0.0040 chunk 109 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.116009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092526 restraints weight = 36816.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.095928 restraints weight = 18645.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098143 restraints weight = 12427.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099584 restraints weight = 9626.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100510 restraints weight = 8154.917| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 17159 Z= 0.114 Angle : 0.669 15.752 23467 Z= 0.312 Chirality : 0.045 0.349 2848 Planarity : 0.003 0.047 2826 Dihedral : 7.813 95.096 3861 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 3.28 % Allowed : 21.53 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1929 helix: 1.51 (0.26), residues: 405 sheet: 0.50 (0.23), residues: 504 loop : -0.44 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 337 TYR 0.015 0.001 TYR B 435 PHE 0.025 0.001 PHE A 522 TRP 0.015 0.001 TRP A 631 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17037) covalent geometry : angle 0.59957 / 0.29 (23139) SS BOND : bond 0.00699 / 0.54 ( 38) SS BOND : angle 2.92814 / 2.12 ( 76) hydrogen bonds : bond 0.03655 / 2.42 ( 598) hydrogen bonds : angle 5.41811 / 3.74 ( 1659) link_ALPHA1-3 : bond 0.01187 / 0.57 ( 5) link_ALPHA1-3 : angle 2.24600 / 1.85 ( 15) link_ALPHA1-6 : bond 0.01859 / 0.93 ( 3) link_ALPHA1-6 : angle 3.32875 / 2.39 ( 9) link_BETA1-4 : bond 0.00395 / 0.21 ( 23) link_BETA1-4 : angle 1.72089 / 1.12 ( 69) link_BETA1-6 : bond 0.00343 / 0.18 ( 1) link_BETA1-6 : angle 0.65674 / 0.37 ( 3) link_NAG-ASN : bond 0.00403 / 0.26 ( 52) link_NAG-ASN : angle 2.71321 / 1.73 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7147 (tmtt) REVERT: A 373 THR cc_start: 0.8396 (p) cc_final: 0.7975 (t) REVERT: A 452 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7925 (mt) REVERT: B 151 ARG cc_start: 0.7431 (ttt180) cc_final: 0.6625 (tpm170) REVERT: B 564 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5352 (t70) REVERT: C 426 MET cc_start: 0.8213 (tpp) cc_final: 0.7875 (tpt) REVERT: C 465 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6759 (p0) REVERT: C 637 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.6203 (t0) REVERT: H 99 GLU cc_start: 0.8145 (tp30) cc_final: 0.7670 (mm-30) REVERT: L 17 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7880 (mt-10) REVERT: L 31 TYR cc_start: 0.7514 (m-80) cc_final: 0.7212 (m-10) REVERT: L 45 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7991 (mtm110) REVERT: L 61 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (ptt-90) outliers start: 57 outliers final: 42 residues processed: 220 average time/residue: 0.1205 time to fit residues: 41.1109 Evaluate side-chains 207 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 577 GLN C 563 GLN L 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.114113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091502 restraints weight = 36105.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.094773 restraints weight = 17738.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096955 restraints weight = 11600.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098356 restraints weight = 8872.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099261 restraints weight = 7452.975| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17159 Z= 0.157 Angle : 0.692 17.229 23467 Z= 0.323 Chirality : 0.045 0.341 2848 Planarity : 0.004 0.047 2826 Dihedral : 7.750 93.913 3861 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 3.97 % Allowed : 21.36 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1929 helix: 1.58 (0.26), residues: 399 sheet: 0.49 (0.23), residues: 508 loop : -0.47 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 337 TYR 0.020 0.001 TYR B 435 PHE 0.026 0.002 PHE A 522 TRP 0.016 0.001 TRP A 631 HIS 0.005 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (17037) covalent geometry : angle 0.62142 / 0.30 (23139) SS BOND : bond 0.00829 / 0.63 ( 38) SS BOND : angle 3.06755 / 2.21 ( 76) hydrogen bonds : bond 0.03752 / 2.50 ( 598) hydrogen bonds : angle 5.42496 / 3.74 ( 1659) link_ALPHA1-3 : bond 0.01091 / 0.53 ( 5) link_ALPHA1-3 : angle 2.28228 / 1.85 ( 15) link_ALPHA1-6 : bond 0.01762 / 0.88 ( 3) link_ALPHA1-6 : angle 3.29437 / 2.36 ( 9) link_BETA1-4 : bond 0.00351 / 0.19 ( 23) link_BETA1-4 : angle 1.74861 / 1.15 ( 69) link_BETA1-6 : bond 0.00366 / 0.19 ( 1) link_BETA1-6 : angle 1.03677 / 0.60 ( 3) link_NAG-ASN : bond 0.00472 / 0.30 ( 52) link_NAG-ASN : angle 2.76549 / 1.77 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 168 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7108 (tmtt) REVERT: A 373 THR cc_start: 0.8495 (p) cc_final: 0.8064 (t) REVERT: A 377 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 452 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7949 (mt) REVERT: B 151 ARG cc_start: 0.7437 (ttt180) cc_final: 0.6635 (tpm170) REVERT: B 161 MET cc_start: 0.7946 (tpt) cc_final: 0.7487 (tpt) REVERT: B 564 HIS cc_start: 0.6005 (OUTLIER) cc_final: 0.5345 (t70) REVERT: C 426 MET cc_start: 0.8234 (tpp) cc_final: 0.7889 (tpt) REVERT: C 465 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6761 (p0) REVERT: C 637 ASN cc_start: 0.7458 (OUTLIER) cc_final: 0.6219 (t0) REVERT: H 99 GLU cc_start: 0.8149 (tp30) cc_final: 0.7699 (mm-30) REVERT: L 17 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7895 (mt-10) REVERT: L 45 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7933 (mtm110) outliers start: 69 outliers final: 50 residues processed: 218 average time/residue: 0.1235 time to fit residues: 42.2836 Evaluate side-chains 214 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 152 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.114357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091907 restraints weight = 36219.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095177 restraints weight = 17694.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097294 restraints weight = 11549.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098696 restraints weight = 8856.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099612 restraints weight = 7427.860| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17159 Z= 0.167 Angle : 0.704 18.511 23467 Z= 0.329 Chirality : 0.045 0.342 2848 Planarity : 0.004 0.045 2826 Dihedral : 7.944 91.822 3861 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 3.74 % Allowed : 21.42 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 1929 helix: 1.64 (0.26), residues: 393 sheet: 0.45 (0.23), residues: 505 loop : -0.48 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 337 TYR 0.021 0.001 TYR B 643 PHE 0.027 0.002 PHE A 522 TRP 0.031 0.001 TRP B 631 HIS 0.004 0.001 HIS L 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (17037) covalent geometry : angle 0.63413 / 0.31 (23139) SS BOND : bond 0.00818 / 0.62 ( 38) SS BOND : angle 3.09428 / 2.23 ( 76) hydrogen bonds : bond 0.03790 / 2.53 ( 598) hydrogen bonds : angle 5.43260 / 3.75 ( 1659) link_ALPHA1-3 : bond 0.01177 / 0.57 ( 5) link_ALPHA1-3 : angle 2.33524 / 1.87 ( 15) link_ALPHA1-6 : bond 0.01615 / 0.81 ( 3) link_ALPHA1-6 : angle 3.28581 / 2.33 ( 9) link_BETA1-4 : bond 0.00353 / 0.19 ( 23) link_BETA1-4 : angle 1.74770 / 1.15 ( 69) link_BETA1-6 : bond 0.00442 / 0.23 ( 1) link_BETA1-6 : angle 1.20993 / 0.68 ( 3) link_NAG-ASN : bond 0.00469 / 0.31 ( 52) link_NAG-ASN : angle 2.79061 / 1.79 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 168 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7144 (tmtt) REVERT: A 373 THR cc_start: 0.8529 (p) cc_final: 0.8096 (t) REVERT: A 452 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7953 (mt) REVERT: B 151 ARG cc_start: 0.7450 (ttt180) cc_final: 0.6619 (tpm170) REVERT: B 161 MET cc_start: 0.7973 (tpt) cc_final: 0.7495 (tpt) REVERT: B 370 GLU cc_start: 0.7653 (mp0) cc_final: 0.7339 (mp0) REVERT: B 434 MET cc_start: 0.8088 (ttp) cc_final: 0.7790 (ttp) REVERT: B 564 HIS cc_start: 0.6092 (OUTLIER) cc_final: 0.5408 (t70) REVERT: B 624 ASN cc_start: 0.7989 (t0) cc_final: 0.7714 (t0) REVERT: C 426 MET cc_start: 0.8230 (tpp) cc_final: 0.7886 (tpt) REVERT: C 465 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6793 (p0) REVERT: C 637 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.6238 (t0) REVERT: H 99 GLU cc_start: 0.8157 (tp30) cc_final: 0.7701 (mm-30) REVERT: L 13 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7535 (tp) REVERT: L 17 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7774 (mt-10) REVERT: L 45 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7919 (mtm110) outliers start: 65 outliers final: 51 residues processed: 213 average time/residue: 0.1272 time to fit residues: 42.4602 Evaluate side-chains 219 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 185 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090302 restraints weight = 36905.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093605 restraints weight = 18812.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095736 restraints weight = 12648.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097151 restraints weight = 9887.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097971 restraints weight = 8382.659| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17159 Z= 0.176 Angle : 0.710 18.249 23467 Z= 0.333 Chirality : 0.045 0.337 2848 Planarity : 0.004 0.046 2826 Dihedral : 8.042 91.325 3861 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 3.80 % Allowed : 21.42 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1929 helix: 1.63 (0.26), residues: 393 sheet: 0.44 (0.23), residues: 505 loop : -0.49 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 337 TYR 0.021 0.001 TYR B 435 PHE 0.029 0.002 PHE A 522 TRP 0.033 0.001 TRP B 631 HIS 0.004 0.001 HIS C 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (17037) covalent geometry : angle 0.63949 / 0.31 (23139) SS BOND : bond 0.00857 / 0.63 ( 38) SS BOND : angle 3.11018 / 2.26 ( 76) hydrogen bonds : bond 0.03830 / 2.56 ( 598) hydrogen bonds : angle 5.44680 / 3.75 ( 1659) link_ALPHA1-3 : bond 0.01108 / 0.53 ( 5) link_ALPHA1-3 : angle 2.29687 / 1.84 ( 15) link_ALPHA1-6 : bond 0.01445 / 0.72 ( 3) link_ALPHA1-6 : angle 3.22549 / 2.27 ( 9) link_BETA1-4 : bond 0.00342 / 0.19 ( 23) link_BETA1-4 : angle 1.77864 / 1.17 ( 69) link_BETA1-6 : bond 0.00423 / 0.22 ( 1) link_BETA1-6 : angle 1.15125 / 0.65 ( 3) link_NAG-ASN : bond 0.00478 / 0.31 ( 52) link_NAG-ASN : angle 2.81758 / 1.81 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8364 (mmmt) cc_final: 0.7154 (tmtt) REVERT: A 218 CYS cc_start: 0.5903 (m) cc_final: 0.5632 (m) REVERT: A 373 THR cc_start: 0.8548 (p) cc_final: 0.8132 (t) REVERT: A 452 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7994 (mt) REVERT: B 151 ARG cc_start: 0.7460 (ttt180) cc_final: 0.6603 (tpm170) REVERT: B 370 GLU cc_start: 0.7635 (mp0) cc_final: 0.7391 (mp0) REVERT: B 434 MET cc_start: 0.8130 (ttp) cc_final: 0.7844 (ttp) REVERT: B 564 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5467 (t70) REVERT: B 624 ASN cc_start: 0.7949 (t0) cc_final: 0.7608 (t0) REVERT: B 631 TRP cc_start: 0.8456 (t-100) cc_final: 0.8251 (t-100) REVERT: C 426 MET cc_start: 0.8205 (tpp) cc_final: 0.7865 (tpt) REVERT: C 465 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6831 (p0) REVERT: C 490 GLU cc_start: 0.7879 (pt0) cc_final: 0.7340 (pp20) REVERT: C 637 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.6248 (t0) REVERT: H 99 GLU cc_start: 0.8151 (tp30) cc_final: 0.7707 (mm-30) REVERT: L 13 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7517 (tp) REVERT: L 17 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7802 (mt-10) REVERT: L 45 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7938 (mtm110) outliers start: 66 outliers final: 54 residues processed: 218 average time/residue: 0.1219 time to fit residues: 41.8382 Evaluate side-chains 222 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 85 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 0.0010 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.091089 restraints weight = 36075.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094356 restraints weight = 17947.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.096503 restraints weight = 11798.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097879 restraints weight = 9056.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098789 restraints weight = 7622.068| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 17159 Z= 0.250 Angle : 0.898 59.192 23467 Z= 0.479 Chirality : 0.046 0.569 2848 Planarity : 0.004 0.073 2826 Dihedral : 8.064 92.824 3861 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 3.86 % Allowed : 21.65 % Favored : 74.50 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1929 helix: 1.64 (0.26), residues: 393 sheet: 0.43 (0.23), residues: 505 loop : -0.49 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 337 TYR 0.031 0.001 TYR L 91 PHE 0.027 0.002 PHE A 522 TRP 0.028 0.001 TRP B 631 HIS 0.006 0.001 HIS C 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (17037) covalent geometry : angle 0.83978 / 0.46 (23139) SS BOND : bond 0.01233 / 0.93 ( 38) SS BOND : angle 3.55015 / 2.49 ( 76) hydrogen bonds : bond 0.03814 / 2.55 ( 598) hydrogen bonds : angle 5.46185 / 3.76 ( 1659) link_ALPHA1-3 : bond 0.00940 / 0.45 ( 5) link_ALPHA1-3 : angle 2.49628 / 2.04 ( 15) link_ALPHA1-6 : bond 0.01422 / 0.71 ( 3) link_ALPHA1-6 : angle 3.22368 / 2.27 ( 9) link_BETA1-4 : bond 0.00332 / 0.18 ( 23) link_BETA1-4 : angle 1.77373 / 1.17 ( 69) link_BETA1-6 : bond 0.00526 / 0.28 ( 1) link_BETA1-6 : angle 1.01812 / 0.58 ( 3) link_NAG-ASN : bond 0.00471 / 0.31 ( 52) link_NAG-ASN : angle 2.81488 / 1.81 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.75 seconds wall clock time: 50 minutes 25.60 seconds (3025.60 seconds total)