Starting phenix.real_space_refine on Wed May 21 11:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfg_33789/05_2025/7yfg_33789_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfg_33789/05_2025/7yfg_33789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfg_33789/05_2025/7yfg_33789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfg_33789/05_2025/7yfg_33789.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfg_33789/05_2025/7yfg_33789_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfg_33789/05_2025/7yfg_33789_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 98 5.16 5 C 13413 2.51 5 N 3656 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21215 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5185 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 29, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5045 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 Chain: "C" Number of atoms: 5238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5238 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 30, 'TRANS': 628} Chain breaks: 1 Chain: "D" Number of atoms: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5048 Classifications: {'peptide': 652} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 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: "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: "G" 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: 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: "O" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" 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: "n" 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.84, per 1000 atoms: 0.56 Number of scatterers: 21215 At special positions: 0 Unit cell: (122.094, 149.94, 133.875, 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 98 16.00 O 4048 8.00 N 3656 7.00 C 13413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.04 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " 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=1, symmetry=0 Links applied ALPHA1-4 " NAG H 2 " - " MAN H 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG S 1 " - " NAG S 2 " " NAG X 1 " - " NAG X 2 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG k 1 " - " NAG k 2 " " NAG n 1 " - " NAG n 2 " " NAG q 1 " - " NAG q 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 901 " - " ASN A 300 " " NAG A 902 " - " ASN A 491 " " NAG A 903 " - " ASN A 440 " " NAG B 901 " - " ASN B 685 " " NAG B 902 " - " ASN B 70 " " NAG B 903 " - " ASN B 438 " " NAG C 901 " - " ASN C 300 " " NAG C 902 " - " ASN C 350 " " NAG C 903 " - " ASN C 491 " " NAG C 904 " - " ASN C 440 " " NAG D 901 " - " ASN D 685 " " NAG D 902 " - " ASN D 70 " " NAG D 903 " - " ASN D 438 " " NAG E 1 " - " ASN A 276 " " NAG G 1 " - " ASN A 771 " " NAG H 1 " - " ASN A 368 " " NAG J 1 " - " ASN A 350 " " NAG K 1 " - " ASN A 61 " " NAG M 1 " - " ASN A 203 " " NAG O 1 " - " ASN A 239 " " NAG S 1 " - " ASN A 471 " " NAG X 1 " - " ASN B 337 " " NAG a 1 " - " ASN C 61 " " NAG c 1 " - " ASN C 203 " " NAG e 1 " - " ASN C 239 " " NAG g 1 " - " ASN C 276 " " NAG k 1 " - " ASN C 771 " " NAG n 1 " - " ASN C 471 " " NAG q 1 " - " ASN C 368 " " NAG v 1 " - " ASN D 337 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.68 Conformation dependent library (CDL) restraints added in 2.4 seconds 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 32 sheets defined 37.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.503A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.031A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.942A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.767A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.985A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.547A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.675A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 744 removed outlier: 3.754A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.546A pdb=" N VAL A 772 " --> pdb=" O TRP A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.567A pdb=" N ARG B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.610A pdb=" N ALA B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.611A pdb=" N GLN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.833A pdb=" N GLN B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.794A pdb=" N ASN B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 696 through 707 removed outlier: 4.226A pdb=" N LYS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE B 706 " --> pdb=" O HIS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 730 through 740 Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 784 through 794 Processing helix chain 'C' and resid 37 through 53 removed outlier: 3.539A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.659A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.834A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.941A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.918A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.594A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.521A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 276 through 296 Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 526 removed outlier: 4.126A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.777A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 724 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.647A pdb=" N LEU D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 removed outlier: 4.225A pdb=" N SER D 126 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 128 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.529A pdb=" N GLN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 188 Processing helix chain 'D' and resid 208 through 217 removed outlier: 4.311A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 284 through 308 Processing helix chain 'D' and resid 325 through 337 removed outlier: 4.082A pdb=" N ASN D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 520 removed outlier: 3.871A pdb=" N ILE D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 696 through 704 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.558A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.637A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 7.858A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.919A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.383A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.556A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.895A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.765A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.319A pdb=" N VAL B 30 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU B 65 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 93 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE B 122 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 95 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.923A pdb=" N PHE B 165 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 198 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B 167 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 200 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 169 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 223 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 276 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 477 removed outlier: 6.928A pdb=" N LEU B 403 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR B 476 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL B 405 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 505 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.948A pdb=" N THR B 450 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.056A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.056A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 527 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY B 758 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 529 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR B 756 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.956A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 32 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.604A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.549A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.626A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 413 removed outlier: 6.184A pdb=" N ILE C 435 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU C 478 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR C 437 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC3, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.010A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.555A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 64 through 66 removed outlier: 6.803A pdb=" N ILE D 93 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 122 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE D 95 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 198 through 200 removed outlier: 8.981A pdb=" N LEU D 199 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 167 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 274 through 278 removed outlier: 6.562A pdb=" N MET D 358 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG D 374 " --> pdb=" O MET D 358 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL D 360 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AC9, first strand: chain 'D' and resid 389 through 390 removed outlier: 4.272A pdb=" N ARG D 389 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 472 through 477 removed outlier: 3.843A pdb=" N VAL D 405 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 415 through 417 Processing sheet with id=AD3, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AD4, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.666A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.666A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 527 " --> pdb=" O GLY D 758 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY D 758 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR D 529 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 756 " --> pdb=" O THR D 529 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.00 Time building geometry restraints manager: 6.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.21: 8 1.21 - 1.51: 13639 1.51 - 1.82: 8024 1.82 - 2.12: 1 2.12 - 2.42: 1 Bond restraints: 21673 Sorted by residual: bond pdb=" N PRO C 670 " pdb=" CD PRO C 670 " ideal model delta sigma weight residual 1.473 0.942 0.531 1.40e-02 5.10e+03 1.44e+03 bond pdb=" CB PRO D 676 " pdb=" CG PRO D 676 " ideal model delta sigma weight residual 1.492 2.421 -0.929 5.00e-02 4.00e+02 3.45e+02 bond pdb=" CG PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 1.503 0.907 0.596 3.40e-02 8.65e+02 3.07e+02 bond pdb=" CB PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 1.492 0.965 0.527 5.00e-02 4.00e+02 1.11e+02 bond pdb=" CG PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 1.503 1.145 0.358 3.40e-02 8.65e+02 1.11e+02 ... (remaining 21668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 29397 21.22 - 42.44: 7 42.44 - 63.66: 1 63.66 - 84.88: 0 84.88 - 106.09: 1 Bond angle restraints: 29406 Sorted by residual: angle pdb=" CB PRO D 676 " pdb=" CG PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO B 59 " pdb=" CD PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 103.20 73.25 29.95 1.50e+00 4.44e-01 3.99e+02 angle pdb=" CA PRO B 59 " pdb=" CB PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 104.50 68.69 35.81 1.90e+00 2.77e-01 3.55e+02 angle pdb=" N PRO A 304 " pdb=" CD PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 103.20 76.00 27.20 1.50e+00 4.44e-01 3.29e+02 angle pdb=" CA PRO D 676 " pdb=" N PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 112.00 87.87 24.13 1.40e+00 5.10e-01 2.97e+02 ... (remaining 29401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 12494 24.40 - 48.81: 935 48.81 - 73.21: 141 73.21 - 97.62: 54 97.62 - 122.02: 11 Dihedral angle restraints: 13635 sinusoidal: 6094 harmonic: 7541 Sorted by residual: dihedral pdb=" CA GLU C 299 " pdb=" C GLU C 299 " pdb=" N ASN C 300 " pdb=" CA ASN C 300 " ideal model delta harmonic sigma weight residual 180.00 -142.51 -37.49 0 5.00e+00 4.00e-02 5.62e+01 dihedral pdb=" CB CYS D 82 " pdb=" SG CYS D 82 " pdb=" SG CYS D 317 " pdb=" CB CYS D 317 " ideal model delta sinusoidal sigma weight residual 93.00 150.30 -57.30 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" N PRO B 59 " pdb=" CG PRO B 59 " pdb=" CD PRO B 59 " pdb=" CB PRO B 59 " ideal model delta sinusoidal sigma weight residual 30.00 108.98 -78.98 1 1.50e+01 4.44e-03 3.45e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3354 0.120 - 0.239: 66 0.239 - 0.359: 4 0.359 - 0.479: 1 0.479 - 0.599: 4 Chirality restraints: 3429 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.88e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.15e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.60 2.00e-01 2.50e+01 8.96e+00 ... (remaining 3426 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 239 " -0.344 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" CG ASN A 239 " 0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN A 239 " 0.096 2.00e-02 2.50e+03 pdb=" ND2 ASN A 239 " 0.484 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 904 " -0.318 2.00e-02 2.50e+03 2.67e-01 8.91e+02 pdb=" C7 NAG C 904 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 904 " -0.190 2.00e-02 2.50e+03 pdb=" N2 NAG C 904 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG C 904 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.86e+02 pdb=" C7 NAG O 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.047 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 216 2.61 - 3.18: 18438 3.18 - 3.75: 31888 3.75 - 4.33: 43390 4.33 - 4.90: 73031 Nonbonded interactions: 166963 Sorted by model distance: nonbonded pdb=" O ARG A 36 " pdb=" NH1 ARG A 36 " model vdw 2.035 3.120 nonbonded pdb=" OD1 ASN C 300 " pdb=" C1 NAG C 901 " model vdw 2.045 2.776 nonbonded pdb=" OE1 GLU B 410 " pdb=" OG SER B 509 " model vdw 2.054 3.040 nonbonded pdb=" O THR D 791 " pdb=" OG SER D 795 " model vdw 2.125 3.040 nonbonded pdb=" OD2 ASP C 732 " pdb=" N GLY C 905 " model vdw 2.155 3.120 ... (remaining 166958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 25 through 545 or resid 663 through 794 or resid 902 throu \ gh 905)) } ncs_group { reference = (chain 'B' and (resid 29 through 537 or resid 658 through 799 or resid 901 throu \ gh 904)) selection = (chain 'D' and (resid 29 through 799 or resid 901 through 904)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'k' selection = chain 'n' selection = chain 'q' 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.300 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.012 0.929 21734 Z= 0.478 Angle : 1.183 106.094 29574 Z= 0.565 Chirality : 0.052 0.599 3429 Planarity : 0.010 0.267 3725 Dihedral : 17.446 122.025 8751 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.92 % Rotamer: Outliers : 0.22 % Allowed : 21.19 % Favored : 78.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2600 helix: 1.11 (0.17), residues: 924 sheet: -1.26 (0.24), residues: 444 loop : -1.78 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 381 HIS 0.008 0.001 HIS C 371 PHE 0.012 0.001 PHE C 197 TYR 0.033 0.001 TYR D 675 ARG 0.022 0.001 ARG B 209 Details of bonding type rmsd link_NAG-ASN : bond 0.11053 ( 30) link_NAG-ASN : angle 5.75676 ( 90) link_ALPHA1-4 : bond 0.01024 ( 1) link_ALPHA1-4 : angle 1.81246 ( 3) link_BETA1-4 : bond 0.00470 ( 17) link_BETA1-4 : angle 0.98321 ( 51) hydrogen bonds : bond 0.14449 ( 822) hydrogen bonds : angle 6.99174 ( 2376) SS BOND : bond 0.00289 ( 12) SS BOND : angle 0.70516 ( 24) covalent geometry : bond 0.01121 (21673) covalent geometry : angle 1.14212 (29406) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 192 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 443 SER cc_start: 0.3218 (OUTLIER) cc_final: 0.3009 (t) REVERT: D 371 MET cc_start: 0.8435 (tmm) cc_final: 0.7660 (ttp) outliers start: 5 outliers final: 1 residues processed: 197 average time/residue: 0.3434 time to fit residues: 104.7877 Evaluate side-chains 185 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN C 371 HIS D 43 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 439 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116395 restraints weight = 31145.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117981 restraints weight = 32802.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119119 restraints weight = 23251.703| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 21734 Z= 0.151 Angle : 0.646 13.498 29574 Z= 0.319 Chirality : 0.046 0.442 3429 Planarity : 0.005 0.095 3725 Dihedral : 9.861 111.483 3862 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 3.43 % Allowed : 19.50 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2600 helix: 1.28 (0.17), residues: 938 sheet: -1.32 (0.24), residues: 424 loop : -1.67 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 281 HIS 0.005 0.001 HIS D 301 PHE 0.012 0.001 PHE A 458 TYR 0.018 0.001 TYR D 675 ARG 0.005 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 30) link_NAG-ASN : angle 3.24485 ( 90) link_ALPHA1-4 : bond 0.00435 ( 1) link_ALPHA1-4 : angle 2.19163 ( 3) link_BETA1-4 : bond 0.00545 ( 17) link_BETA1-4 : angle 1.48941 ( 51) hydrogen bonds : bond 0.03884 ( 822) hydrogen bonds : angle 5.48196 ( 2376) SS BOND : bond 0.00246 ( 12) SS BOND : angle 0.89704 ( 24) covalent geometry : bond 0.00364 (21673) covalent geometry : angle 0.61887 (29406) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 199 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.6910 (mm) cc_final: 0.6386 (mm) REVERT: A 67 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7725 (m90) REVERT: A 166 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7623 (tt) REVERT: A 354 MET cc_start: 0.7779 (mmm) cc_final: 0.7333 (mmm) REVERT: A 667 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8303 (pp) REVERT: A 755 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: B 108 LEU cc_start: 0.8854 (mm) cc_final: 0.8364 (mm) REVERT: B 171 LEU cc_start: 0.7914 (mt) cc_final: 0.7667 (tp) REVERT: C 209 MET cc_start: 0.7413 (mmm) cc_final: 0.6926 (mmt) REVERT: D 371 MET cc_start: 0.8497 (tmm) cc_final: 0.7921 (ttp) outliers start: 77 outliers final: 42 residues processed: 258 average time/residue: 0.3135 time to fit residues: 127.1596 Evaluate side-chains 227 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 9 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 86 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114965 restraints weight = 31063.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116353 restraints weight = 30084.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117297 restraints weight = 23738.701| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21734 Z= 0.148 Angle : 0.603 12.001 29574 Z= 0.299 Chirality : 0.045 0.436 3429 Planarity : 0.004 0.083 3725 Dihedral : 8.934 109.874 3861 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 3.12 % Allowed : 19.86 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2600 helix: 1.29 (0.17), residues: 946 sheet: -1.28 (0.24), residues: 422 loop : -1.59 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.006 0.001 HIS A 53 PHE 0.015 0.001 PHE A 458 TYR 0.023 0.001 TYR D 675 ARG 0.004 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 30) link_NAG-ASN : angle 3.07470 ( 90) link_ALPHA1-4 : bond 0.00312 ( 1) link_ALPHA1-4 : angle 2.12650 ( 3) link_BETA1-4 : bond 0.00476 ( 17) link_BETA1-4 : angle 1.43478 ( 51) hydrogen bonds : bond 0.03666 ( 822) hydrogen bonds : angle 5.28300 ( 2376) SS BOND : bond 0.00257 ( 12) SS BOND : angle 1.24291 ( 24) covalent geometry : bond 0.00348 (21673) covalent geometry : angle 0.57620 (29406) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 190 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7654 (m90) REVERT: A 166 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7663 (tt) REVERT: A 342 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6374 (tp30) REVERT: A 354 MET cc_start: 0.7791 (mmm) cc_final: 0.7335 (mmm) REVERT: A 667 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8269 (pp) REVERT: B 108 LEU cc_start: 0.8848 (mm) cc_final: 0.8337 (mm) REVERT: B 171 LEU cc_start: 0.7899 (mt) cc_final: 0.7695 (tp) REVERT: B 699 MET cc_start: 0.7816 (ttt) cc_final: 0.7594 (ttt) REVERT: C 209 MET cc_start: 0.7501 (mmm) cc_final: 0.7037 (mmt) REVERT: C 371 HIS cc_start: 0.7493 (m-70) cc_final: 0.7206 (m170) REVERT: C 795 TYR cc_start: 0.6866 (m-10) cc_final: 0.6565 (m-80) REVERT: D 371 MET cc_start: 0.8292 (tmm) cc_final: 0.8078 (ttp) outliers start: 70 outliers final: 45 residues processed: 245 average time/residue: 0.3072 time to fit residues: 118.9765 Evaluate side-chains 228 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 258 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 chunk 251 optimal weight: 0.0470 chunk 230 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 HIS C 709 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114819 restraints weight = 31459.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116266 restraints weight = 33428.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117472 restraints weight = 23947.072| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21734 Z= 0.144 Angle : 0.593 11.856 29574 Z= 0.293 Chirality : 0.045 0.435 3429 Planarity : 0.004 0.083 3725 Dihedral : 8.245 108.009 3859 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 3.92 % Allowed : 19.95 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2600 helix: 1.33 (0.17), residues: 944 sheet: -1.29 (0.24), residues: 424 loop : -1.54 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.006 0.001 HIS A 67 PHE 0.013 0.001 PHE A 458 TYR 0.019 0.001 TYR D 675 ARG 0.004 0.000 ARG A 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 30) link_NAG-ASN : angle 2.97638 ( 90) link_ALPHA1-4 : bond 0.00289 ( 1) link_ALPHA1-4 : angle 2.24364 ( 3) link_BETA1-4 : bond 0.00494 ( 17) link_BETA1-4 : angle 1.46404 ( 51) hydrogen bonds : bond 0.03489 ( 822) hydrogen bonds : angle 5.16868 ( 2376) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.04564 ( 24) covalent geometry : bond 0.00341 (21673) covalent geometry : angle 0.56675 (29406) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 194 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7466 (m90) REVERT: A 166 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7693 (tt) REVERT: A 345 ASP cc_start: 0.6598 (m-30) cc_final: 0.6222 (m-30) REVERT: A 354 MET cc_start: 0.7776 (mmm) cc_final: 0.7309 (mmm) REVERT: A 667 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8251 (pp) REVERT: A 755 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7271 (mmm160) REVERT: B 108 LEU cc_start: 0.8865 (mm) cc_final: 0.8302 (mm) REVERT: B 134 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: B 746 VAL cc_start: 0.5235 (OUTLIER) cc_final: 0.5028 (m) REVERT: C 209 MET cc_start: 0.7546 (mmm) cc_final: 0.7065 (mmt) REVERT: C 371 HIS cc_start: 0.7483 (m-70) cc_final: 0.7270 (m-70) REVERT: C 492 ASN cc_start: 0.3034 (OUTLIER) cc_final: 0.2346 (p0) REVERT: C 795 TYR cc_start: 0.6870 (m-10) cc_final: 0.6548 (m-80) REVERT: D 371 MET cc_start: 0.8298 (tmm) cc_final: 0.8086 (ttp) REVERT: D 675 TYR cc_start: 0.5645 (OUTLIER) cc_final: 0.4660 (m-80) REVERT: D 678 PHE cc_start: 0.5197 (OUTLIER) cc_final: 0.4730 (t80) outliers start: 88 outliers final: 57 residues processed: 262 average time/residue: 0.3014 time to fit residues: 125.9320 Evaluate side-chains 248 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 143 optimal weight: 0.9980 chunk 69 optimal weight: 0.0870 chunk 33 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 245 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116402 restraints weight = 31102.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118338 restraints weight = 29179.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119124 restraints weight = 22298.231| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21734 Z= 0.104 Angle : 0.580 14.169 29574 Z= 0.282 Chirality : 0.044 0.418 3429 Planarity : 0.004 0.083 3725 Dihedral : 7.456 105.155 3859 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 3.03 % Allowed : 21.33 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2600 helix: 1.47 (0.17), residues: 944 sheet: -1.17 (0.24), residues: 422 loop : -1.45 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A 53 PHE 0.012 0.001 PHE A 458 TYR 0.020 0.001 TYR D 675 ARG 0.004 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 30) link_NAG-ASN : angle 3.49690 ( 90) link_ALPHA1-4 : bond 0.00309 ( 1) link_ALPHA1-4 : angle 2.37682 ( 3) link_BETA1-4 : bond 0.00622 ( 17) link_BETA1-4 : angle 1.57606 ( 51) hydrogen bonds : bond 0.03100 ( 822) hydrogen bonds : angle 5.01014 ( 2376) SS BOND : bond 0.00281 ( 12) SS BOND : angle 0.82457 ( 24) covalent geometry : bond 0.00227 (21673) covalent geometry : angle 0.54345 (29406) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6228 (mm) REVERT: A 67 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7375 (m90) REVERT: A 345 ASP cc_start: 0.6569 (m-30) cc_final: 0.6317 (m-30) REVERT: A 354 MET cc_start: 0.7762 (mmm) cc_final: 0.7301 (mmm) REVERT: A 448 ARG cc_start: 0.5984 (mmt90) cc_final: 0.5078 (ptt180) REVERT: A 667 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 752 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 755 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7975 (mtt-85) REVERT: B 108 LEU cc_start: 0.8818 (mm) cc_final: 0.8346 (mm) REVERT: C 370 THR cc_start: 0.8158 (m) cc_final: 0.7935 (p) REVERT: C 795 TYR cc_start: 0.6749 (m-10) cc_final: 0.6520 (m-80) REVERT: D 371 MET cc_start: 0.8267 (tmm) cc_final: 0.8007 (ttt) REVERT: D 675 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.4621 (m-80) REVERT: D 678 PHE cc_start: 0.5112 (OUTLIER) cc_final: 0.4723 (t80) outliers start: 68 outliers final: 36 residues processed: 259 average time/residue: 0.3180 time to fit residues: 129.7164 Evaluate side-chains 230 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 138 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 97 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 chunk 202 optimal weight: 0.0010 chunk 130 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116661 restraints weight = 31178.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117018 restraints weight = 25913.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118157 restraints weight = 24824.145| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21734 Z= 0.101 Angle : 0.559 10.742 29574 Z= 0.274 Chirality : 0.044 0.405 3429 Planarity : 0.004 0.083 3725 Dihedral : 6.919 101.562 3859 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 3.07 % Allowed : 21.24 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2600 helix: 1.52 (0.17), residues: 945 sheet: -1.05 (0.25), residues: 421 loop : -1.42 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 381 HIS 0.004 0.001 HIS A 53 PHE 0.011 0.001 PHE A 458 TYR 0.020 0.001 TYR D 675 ARG 0.007 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 30) link_NAG-ASN : angle 3.10501 ( 90) link_ALPHA1-4 : bond 0.00313 ( 1) link_ALPHA1-4 : angle 2.48553 ( 3) link_BETA1-4 : bond 0.00512 ( 17) link_BETA1-4 : angle 1.31586 ( 51) hydrogen bonds : bond 0.02990 ( 822) hydrogen bonds : angle 4.91326 ( 2376) SS BOND : bond 0.00268 ( 12) SS BOND : angle 0.80728 ( 24) covalent geometry : bond 0.00222 (21673) covalent geometry : angle 0.52943 (29406) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 199 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5973 (mm) REVERT: A 67 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7017 (m90) REVERT: A 166 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 209 MET cc_start: 0.7322 (tpp) cc_final: 0.7051 (mtt) REVERT: A 354 MET cc_start: 0.7723 (mmm) cc_final: 0.7253 (mmm) REVERT: A 667 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8204 (pp) REVERT: A 755 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7208 (mmm160) REVERT: B 108 LEU cc_start: 0.8837 (mm) cc_final: 0.8322 (mm) REVERT: B 709 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6724 (ptt180) REVERT: C 209 MET cc_start: 0.7393 (mmm) cc_final: 0.6826 (mmt) REVERT: C 492 ASN cc_start: 0.3124 (OUTLIER) cc_final: 0.2418 (p0) REVERT: C 795 TYR cc_start: 0.6712 (m-10) cc_final: 0.6473 (m-80) REVERT: D 371 MET cc_start: 0.8333 (tmm) cc_final: 0.8012 (ttt) REVERT: D 675 TYR cc_start: 0.5521 (OUTLIER) cc_final: 0.4535 (m-80) REVERT: D 678 PHE cc_start: 0.5070 (OUTLIER) cc_final: 0.4668 (t80) REVERT: D 723 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6747 (tp) outliers start: 69 outliers final: 45 residues processed: 254 average time/residue: 0.3104 time to fit residues: 127.7276 Evaluate side-chains 242 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 736 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 144 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 247 optimal weight: 0.0070 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115008 restraints weight = 31141.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116962 restraints weight = 30797.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117419 restraints weight = 21904.335| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21734 Z= 0.142 Angle : 0.592 11.224 29574 Z= 0.290 Chirality : 0.045 0.405 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.718 98.784 3859 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 3.47 % Allowed : 20.97 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2600 helix: 1.46 (0.17), residues: 945 sheet: -1.18 (0.25), residues: 416 loop : -1.42 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 498 HIS 0.005 0.001 HIS A 709 PHE 0.018 0.001 PHE D 471 TYR 0.020 0.001 TYR D 675 ARG 0.006 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 30) link_NAG-ASN : angle 3.09045 ( 90) link_ALPHA1-4 : bond 0.00319 ( 1) link_ALPHA1-4 : angle 2.46518 ( 3) link_BETA1-4 : bond 0.00483 ( 17) link_BETA1-4 : angle 1.29699 ( 51) hydrogen bonds : bond 0.03267 ( 822) hydrogen bonds : angle 4.95857 ( 2376) SS BOND : bond 0.00280 ( 12) SS BOND : angle 0.88487 ( 24) covalent geometry : bond 0.00337 (21673) covalent geometry : angle 0.56507 (29406) Misc. bond : bond 0.00942 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6142 (mm) REVERT: A 67 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7467 (m90) REVERT: A 166 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 209 MET cc_start: 0.7308 (tpp) cc_final: 0.6973 (mtt) REVERT: A 354 MET cc_start: 0.7677 (mmm) cc_final: 0.7223 (mmm) REVERT: A 667 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8217 (pp) REVERT: A 755 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7228 (mmm160) REVERT: B 108 LEU cc_start: 0.8827 (mm) cc_final: 0.8286 (mm) REVERT: B 678 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.6024 (t80) REVERT: B 709 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6777 (ptt180) REVERT: C 492 ASN cc_start: 0.2926 (OUTLIER) cc_final: 0.2262 (p0) REVERT: C 795 TYR cc_start: 0.6820 (m-10) cc_final: 0.6572 (m-80) REVERT: D 371 MET cc_start: 0.8339 (tmm) cc_final: 0.8014 (ttt) REVERT: D 675 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4527 (m-80) REVERT: D 678 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4816 (t80) outliers start: 78 outliers final: 54 residues processed: 248 average time/residue: 0.2846 time to fit residues: 113.3926 Evaluate side-chains 242 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 678 PHE Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 237 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 27 optimal weight: 0.1980 chunk 105 optimal weight: 6.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115322 restraints weight = 31252.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116228 restraints weight = 30722.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117234 restraints weight = 23887.086| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21734 Z= 0.102 Angle : 0.564 12.971 29574 Z= 0.276 Chirality : 0.044 0.394 3429 Planarity : 0.004 0.083 3725 Dihedral : 6.279 95.140 3859 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 2.76 % Allowed : 21.77 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2600 helix: 1.52 (0.17), residues: 945 sheet: -1.11 (0.25), residues: 415 loop : -1.39 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 768 HIS 0.006 0.001 HIS A 67 PHE 0.015 0.001 PHE D 471 TYR 0.021 0.001 TYR D 675 ARG 0.006 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 30) link_NAG-ASN : angle 2.99718 ( 90) link_ALPHA1-4 : bond 0.00332 ( 1) link_ALPHA1-4 : angle 2.63446 ( 3) link_BETA1-4 : bond 0.00470 ( 17) link_BETA1-4 : angle 1.18145 ( 51) hydrogen bonds : bond 0.02962 ( 822) hydrogen bonds : angle 4.86334 ( 2376) SS BOND : bond 0.00259 ( 12) SS BOND : angle 0.75091 ( 24) covalent geometry : bond 0.00226 (21673) covalent geometry : angle 0.53789 (29406) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6076 (mm) REVERT: A 67 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7506 (m90) REVERT: A 209 MET cc_start: 0.7310 (tpp) cc_final: 0.7017 (mtt) REVERT: A 354 MET cc_start: 0.7740 (mmm) cc_final: 0.7268 (mmm) REVERT: A 667 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8204 (pp) REVERT: A 755 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7168 (mmm160) REVERT: B 101 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7165 (p) REVERT: B 108 LEU cc_start: 0.8811 (mm) cc_final: 0.8284 (mm) REVERT: B 709 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6752 (ptt180) REVERT: C 209 MET cc_start: 0.7313 (mmm) cc_final: 0.6774 (mmt) REVERT: C 492 ASN cc_start: 0.2980 (OUTLIER) cc_final: 0.2305 (p0) REVERT: C 795 TYR cc_start: 0.6721 (m-10) cc_final: 0.6509 (m-80) REVERT: D 371 MET cc_start: 0.8321 (tmm) cc_final: 0.7989 (ttt) REVERT: D 665 ASP cc_start: 0.4762 (t70) cc_final: 0.4426 (p0) REVERT: D 675 TYR cc_start: 0.5484 (OUTLIER) cc_final: 0.4531 (m-80) REVERT: D 678 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.4721 (t80) REVERT: D 723 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6754 (tp) REVERT: D 774 ASP cc_start: 0.7473 (m-30) cc_final: 0.7172 (m-30) outliers start: 62 outliers final: 40 residues processed: 241 average time/residue: 0.2954 time to fit residues: 114.7466 Evaluate side-chains 233 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 179 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114838 restraints weight = 31085.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116019 restraints weight = 29809.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117188 restraints weight = 23566.563| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21734 Z= 0.113 Angle : 0.574 16.700 29574 Z= 0.281 Chirality : 0.045 0.516 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.072 92.270 3859 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 2.54 % Allowed : 21.99 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2600 helix: 1.53 (0.17), residues: 945 sheet: -1.15 (0.25), residues: 425 loop : -1.35 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 381 HIS 0.006 0.001 HIS A 67 PHE 0.012 0.001 PHE D 471 TYR 0.021 0.001 TYR D 675 ARG 0.005 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 30) link_NAG-ASN : angle 3.08315 ( 90) link_ALPHA1-4 : bond 0.00337 ( 1) link_ALPHA1-4 : angle 2.60681 ( 3) link_BETA1-4 : bond 0.00463 ( 17) link_BETA1-4 : angle 1.14749 ( 51) hydrogen bonds : bond 0.03009 ( 822) hydrogen bonds : angle 4.85860 ( 2376) SS BOND : bond 0.00259 ( 12) SS BOND : angle 0.78897 ( 24) covalent geometry : bond 0.00260 (21673) covalent geometry : angle 0.54669 (29406) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6147 (mm) REVERT: A 44 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6834 (mm-30) REVERT: A 209 MET cc_start: 0.7311 (tpp) cc_final: 0.7017 (mtt) REVERT: A 354 MET cc_start: 0.7721 (mmm) cc_final: 0.7250 (mmm) REVERT: A 667 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8241 (pp) REVERT: A 755 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7180 (mmm160) REVERT: B 108 LEU cc_start: 0.8815 (mm) cc_final: 0.8282 (mm) REVERT: B 709 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6712 (ptt180) REVERT: C 209 MET cc_start: 0.7354 (mmm) cc_final: 0.6819 (mmt) REVERT: C 254 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7959 (pt) REVERT: C 492 ASN cc_start: 0.2956 (OUTLIER) cc_final: 0.2301 (p0) REVERT: D 371 MET cc_start: 0.8335 (tmm) cc_final: 0.8028 (ttt) REVERT: D 675 TYR cc_start: 0.5537 (OUTLIER) cc_final: 0.4539 (m-80) REVERT: D 678 PHE cc_start: 0.5041 (OUTLIER) cc_final: 0.4685 (t80) REVERT: D 723 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6776 (tp) REVERT: D 774 ASP cc_start: 0.7488 (m-30) cc_final: 0.7137 (m-30) outliers start: 57 outliers final: 45 residues processed: 232 average time/residue: 0.2929 time to fit residues: 109.0622 Evaluate side-chains 234 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 736 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 225 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 117 optimal weight: 0.0570 chunk 80 optimal weight: 0.0570 chunk 109 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115409 restraints weight = 31086.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116355 restraints weight = 28746.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117576 restraints weight = 23505.162| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21734 Z= 0.101 Angle : 0.554 10.420 29574 Z= 0.273 Chirality : 0.043 0.385 3429 Planarity : 0.004 0.082 3725 Dihedral : 5.860 89.213 3859 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.63 % Allowed : 22.13 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2600 helix: 1.56 (0.17), residues: 945 sheet: -1.11 (0.25), residues: 425 loop : -1.33 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 381 HIS 0.012 0.001 HIS A 67 PHE 0.012 0.001 PHE D 471 TYR 0.021 0.001 TYR D 675 ARG 0.008 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 30) link_NAG-ASN : angle 2.57808 ( 90) link_ALPHA1-4 : bond 0.00288 ( 1) link_ALPHA1-4 : angle 2.56059 ( 3) link_BETA1-4 : bond 0.00454 ( 17) link_BETA1-4 : angle 1.10865 ( 51) hydrogen bonds : bond 0.02902 ( 822) hydrogen bonds : angle 4.81573 ( 2376) SS BOND : bond 0.00251 ( 12) SS BOND : angle 0.73407 ( 24) covalent geometry : bond 0.00222 (21673) covalent geometry : angle 0.53364 (29406) Misc. bond : bond 0.00138 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 209 MET cc_start: 0.7282 (tpp) cc_final: 0.7043 (mtt) REVERT: A 354 MET cc_start: 0.7703 (mmm) cc_final: 0.7229 (mmm) REVERT: A 667 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8235 (pp) REVERT: A 755 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7918 (mtt-85) REVERT: B 101 THR cc_start: 0.7228 (OUTLIER) cc_final: 0.6916 (p) REVERT: B 108 LEU cc_start: 0.8800 (mm) cc_final: 0.8291 (mm) REVERT: B 678 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.5877 (t80) REVERT: B 709 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6692 (ptt180) REVERT: C 87 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8513 (m) REVERT: C 209 MET cc_start: 0.7379 (mmm) cc_final: 0.6835 (mmt) REVERT: C 254 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7836 (pt) REVERT: C 492 ASN cc_start: 0.2982 (OUTLIER) cc_final: 0.2325 (p0) REVERT: D 371 MET cc_start: 0.8327 (tmm) cc_final: 0.7798 (ttp) REVERT: D 675 TYR cc_start: 0.5623 (OUTLIER) cc_final: 0.4581 (m-80) REVERT: D 678 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.4623 (t80) REVERT: D 723 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6745 (tp) REVERT: D 774 ASP cc_start: 0.7467 (m-30) cc_final: 0.7137 (m-30) outliers start: 59 outliers final: 43 residues processed: 231 average time/residue: 0.3070 time to fit residues: 113.8339 Evaluate side-chains 231 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 678 PHE Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 736 MET Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 252 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 247 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 246 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115514 restraints weight = 31050.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116486 restraints weight = 28699.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117579 restraints weight = 23785.667| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21734 Z= 0.105 Angle : 0.560 10.413 29574 Z= 0.276 Chirality : 0.043 0.381 3429 Planarity : 0.004 0.082 3725 Dihedral : 5.686 85.535 3859 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 2.63 % Allowed : 21.99 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2600 helix: 1.56 (0.17), residues: 945 sheet: -1.13 (0.25), residues: 425 loop : -1.33 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 381 HIS 0.021 0.001 HIS A 709 PHE 0.015 0.001 PHE D 471 TYR 0.020 0.001 TYR D 675 ARG 0.008 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 30) link_NAG-ASN : angle 2.70066 ( 90) link_ALPHA1-4 : bond 0.00356 ( 1) link_ALPHA1-4 : angle 2.44496 ( 3) link_BETA1-4 : bond 0.00444 ( 17) link_BETA1-4 : angle 1.08992 ( 51) hydrogen bonds : bond 0.02919 ( 822) hydrogen bonds : angle 4.81581 ( 2376) SS BOND : bond 0.00437 ( 12) SS BOND : angle 1.40479 ( 24) covalent geometry : bond 0.00236 (21673) covalent geometry : angle 0.53762 (29406) Misc. bond : bond 0.00132 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5405.52 seconds wall clock time: 96 minutes 20.09 seconds (5780.09 seconds total)