Starting phenix.real_space_refine on Mon Apr 6 18:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfg_33789/04_2026/7yfg_33789_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfg_33789/04_2026/7yfg_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_33789/04_2026/7yfg_33789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfg_33789/04_2026/7yfg_33789.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfg_33789/04_2026/7yfg_33789_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfg_33789/04_2026/7yfg_33789_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/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: 4.69, per 1000 atoms: 0.22 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 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: 0.67 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: 3.64 Time building geometry restraints manager: 2.37 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 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: 2.420 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: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.670 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- 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 : 10.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (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 ARG 0.022 0.001 ARG B 209 TYR 0.033 0.001 TYR D 675 PHE 0.012 0.001 PHE C 197 TRP 0.010 0.001 TRP C 381 HIS 0.008 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.01121 (21673) covalent geometry : angle 1.14212 (29406) SS BOND : bond 0.00289 ( 12) SS BOND : angle 0.70516 ( 24) hydrogen bonds : bond 0.14449 ( 822) hydrogen bonds : angle 6.99174 ( 2376) Misc. bond : bond 0.00104 ( 1) 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) link_NAG-ASN : bond 0.11053 ( 30) link_NAG-ASN : angle 5.75676 ( 90) *********************** 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 : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 443 SER cc_start: 0.3217 (OUTLIER) cc_final: 0.3008 (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: 0.1422 time to fit residues: 43.7524 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 : 0.704 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3706 r_free = 0.3706 target = 0.144260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115352 restraints weight = 31275.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116682 restraints weight = 33673.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117795 restraints weight = 24767.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118099 restraints weight = 20124.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118401 restraints weight = 19409.965| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 21734 Z= 0.164 Angle : 0.658 13.303 29574 Z= 0.324 Chirality : 0.047 0.448 3429 Planarity : 0.005 0.090 3725 Dihedral : 9.822 111.030 3862 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 3.47 % Allowed : 19.55 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2600 helix: 1.23 (0.17), residues: 939 sheet: -1.34 (0.24), residues: 424 loop : -1.68 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 36 TYR 0.017 0.001 TYR D 675 PHE 0.012 0.001 PHE C 197 TRP 0.016 0.001 TRP D 281 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00395 (21673) covalent geometry : angle 0.63060 (29406) SS BOND : bond 0.00262 ( 12) SS BOND : angle 0.93536 ( 24) hydrogen bonds : bond 0.03817 ( 822) hydrogen bonds : angle 5.46771 ( 2376) Misc. bond : bond 0.00050 ( 1) link_ALPHA1-4 : bond 0.00387 ( 1) link_ALPHA1-4 : angle 2.20965 ( 3) link_BETA1-4 : bond 0.00553 ( 17) link_BETA1-4 : angle 1.58124 ( 51) link_NAG-ASN : bond 0.00614 ( 30) link_NAG-ASN : angle 3.24547 ( 90) *********************** 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: 78 poor density : 198 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.6905 (mm) cc_final: 0.6681 (mm) REVERT: A 67 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7745 (m90) REVERT: A 166 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7650 (tt) REVERT: A 354 MET cc_start: 0.7783 (mmm) cc_final: 0.7333 (mmm) REVERT: A 667 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8307 (pp) REVERT: A 755 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8022 (mtt-85) REVERT: B 108 LEU cc_start: 0.8860 (mm) cc_final: 0.8339 (mm) REVERT: B 171 LEU cc_start: 0.7931 (mt) cc_final: 0.7696 (tp) REVERT: C 209 MET cc_start: 0.7436 (mmm) cc_final: 0.6950 (mmt) REVERT: C 795 TYR cc_start: 0.6884 (m-10) cc_final: 0.6659 (m-80) REVERT: D 371 MET cc_start: 0.8511 (tmm) cc_final: 0.7948 (ttp) outliers start: 78 outliers final: 43 residues processed: 259 average time/residue: 0.1344 time to fit residues: 55.0199 Evaluate side-chains 228 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 256 ASN 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 245 optimal weight: 0.5980 chunk 165 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 112 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3725 r_free = 0.3725 target = 0.145731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117451 restraints weight = 31214.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120047 restraints weight = 29797.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120452 restraints weight = 20851.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120852 restraints weight = 18330.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120996 restraints weight = 17061.595| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 0.047 21734 Z= 0.113 Angle : 0.579 11.565 29574 Z= 0.287 Chirality : 0.044 0.430 3429 Planarity : 0.004 0.084 3725 Dihedral : 8.752 109.191 3861 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.40 % Allowed : 20.61 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2600 helix: 1.36 (0.17), residues: 945 sheet: -1.24 (0.24), residues: 422 loop : -1.55 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 209 TYR 0.025 0.001 TYR D 675 PHE 0.015 0.001 PHE A 458 TRP 0.011 0.001 TRP A 315 HIS 0.009 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00251 (21673) covalent geometry : angle 0.55253 (29406) SS BOND : bond 0.00218 ( 12) SS BOND : angle 1.09940 ( 24) hydrogen bonds : bond 0.03378 ( 822) hydrogen bonds : angle 5.20714 ( 2376) Misc. bond : bond 0.00070 ( 1) link_ALPHA1-4 : bond 0.00306 ( 1) link_ALPHA1-4 : angle 2.17692 ( 3) link_BETA1-4 : bond 0.00461 ( 17) link_BETA1-4 : angle 1.37432 ( 51) link_NAG-ASN : bond 0.00528 ( 30) link_NAG-ASN : angle 2.95854 ( 90) *********************** 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 253 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7534 (m90) REVERT: A 166 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7678 (tt) REVERT: A 354 MET cc_start: 0.7768 (mmm) cc_final: 0.7316 (mmm) REVERT: A 667 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8249 (pp) REVERT: A 755 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7985 (mtt-85) REVERT: B 108 LEU cc_start: 0.8835 (mm) cc_final: 0.8338 (mm) REVERT: B 171 LEU cc_start: 0.7818 (mt) cc_final: 0.7612 (tp) REVERT: C 209 MET cc_start: 0.7448 (mmm) cc_final: 0.6974 (mmt) REVERT: C 371 HIS cc_start: 0.7454 (m-70) cc_final: 0.7172 (m170) REVERT: C 795 TYR cc_start: 0.6798 (m-10) cc_final: 0.6594 (m-80) outliers start: 54 outliers final: 27 residues processed: 241 average time/residue: 0.1420 time to fit residues: 54.3497 Evaluate side-chains 216 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 317 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 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 C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 180 GLU 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 229 optimal weight: 3.9990 chunk 259 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 HIS ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115254 restraints weight = 31382.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117190 restraints weight = 30819.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118028 restraints weight = 23008.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118427 restraints weight = 19123.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118549 restraints weight = 18512.775| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1222 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= 0.130 Angle : 0.578 11.494 29574 Z= 0.285 Chirality : 0.045 0.424 3429 Planarity : 0.004 0.083 3725 Dihedral : 8.091 107.492 3859 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 3.52 % Allowed : 20.66 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2600 helix: 1.41 (0.17), residues: 945 sheet: -1.20 (0.24), residues: 422 loop : -1.50 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 194 TYR 0.018 0.001 TYR D 675 PHE 0.012 0.001 PHE A 458 TRP 0.010 0.001 TRP A 315 HIS 0.006 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00303 (21673) covalent geometry : angle 0.55167 (29406) SS BOND : bond 0.00328 ( 12) SS BOND : angle 1.03327 ( 24) hydrogen bonds : bond 0.03332 ( 822) hydrogen bonds : angle 5.10323 ( 2376) Misc. bond : bond 0.00064 ( 1) link_ALPHA1-4 : bond 0.00261 ( 1) link_ALPHA1-4 : angle 2.28592 ( 3) link_BETA1-4 : bond 0.00494 ( 17) link_BETA1-4 : angle 1.42668 ( 51) link_NAG-ASN : bond 0.00463 ( 30) link_NAG-ASN : angle 2.95280 ( 90) *********************** 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 277 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 198 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7360 (m90) REVERT: A 166 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7664 (tt) REVERT: A 209 MET cc_start: 0.7441 (tpp) cc_final: 0.7134 (mtt) REVERT: A 345 ASP cc_start: 0.6606 (m-30) cc_final: 0.6206 (m-30) REVERT: A 354 MET cc_start: 0.7765 (mmm) cc_final: 0.7292 (mmm) REVERT: A 667 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 755 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7273 (mmm160) REVERT: B 108 LEU cc_start: 0.8852 (mm) cc_final: 0.8339 (mm) REVERT: C 209 MET cc_start: 0.7556 (mmm) cc_final: 0.7069 (mmt) REVERT: C 492 ASN cc_start: 0.3112 (OUTLIER) cc_final: 0.2412 (p0) REVERT: D 675 TYR cc_start: 0.5561 (OUTLIER) cc_final: 0.4598 (m-80) REVERT: D 678 PHE cc_start: 0.5087 (OUTLIER) cc_final: 0.4613 (t80) outliers start: 79 outliers final: 49 residues processed: 261 average time/residue: 0.1387 time to fit residues: 57.6299 Evaluate side-chains 238 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 182 VAL 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 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 152 optimal weight: 3.9990 chunk 259 optimal weight: 0.1980 chunk 209 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** C 53 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 = 0.3703 r_free = 0.3703 target = 0.143893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115569 restraints weight = 31230.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117540 restraints weight = 31377.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118396 restraints weight = 22524.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118477 restraints weight = 20779.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118882 restraints weight = 18728.040| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21734 Z= 0.132 Angle : 0.593 14.090 29574 Z= 0.290 Chirality : 0.045 0.422 3429 Planarity : 0.004 0.083 3725 Dihedral : 7.535 105.667 3859 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 4.10 % Allowed : 19.95 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2600 helix: 1.44 (0.17), residues: 944 sheet: -1.17 (0.24), residues: 422 loop : -1.48 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 209 TYR 0.019 0.001 TYR D 675 PHE 0.012 0.001 PHE A 458 TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00307 (21673) covalent geometry : angle 0.55755 (29406) SS BOND : bond 0.00300 ( 12) SS BOND : angle 0.93476 ( 24) hydrogen bonds : bond 0.03308 ( 822) hydrogen bonds : angle 5.03596 ( 2376) Misc. bond : bond 0.00065 ( 1) link_ALPHA1-4 : bond 0.00308 ( 1) link_ALPHA1-4 : angle 2.30284 ( 3) link_BETA1-4 : bond 0.00590 ( 17) link_BETA1-4 : angle 1.58286 ( 51) link_NAG-ASN : bond 0.00469 ( 30) link_NAG-ASN : angle 3.48864 ( 90) *********************** 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 284 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 192 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6281 (mm) REVERT: A 67 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7340 (m90) REVERT: A 166 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7651 (tt) REVERT: A 209 MET cc_start: 0.7442 (tpp) cc_final: 0.7111 (mtt) REVERT: A 345 ASP cc_start: 0.6638 (m-30) cc_final: 0.6406 (m-30) REVERT: A 354 MET cc_start: 0.7744 (mmm) cc_final: 0.7273 (mmm) REVERT: A 667 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8234 (pp) REVERT: A 755 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7251 (mmm160) REVERT: B 108 LEU cc_start: 0.8843 (mm) cc_final: 0.8319 (mm) REVERT: C 492 ASN cc_start: 0.2983 (OUTLIER) cc_final: 0.2311 (p0) REVERT: D 675 TYR cc_start: 0.5645 (OUTLIER) cc_final: 0.4703 (m-80) REVERT: D 678 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.4764 (t80) outliers start: 92 outliers final: 56 residues processed: 266 average time/residue: 0.1296 time to fit residues: 55.2062 Evaluate side-chains 247 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 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 747 VAL 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 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 475 LEU Chi-restraints excluded: chain B residue 756 THR 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 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 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 C residue 709 HIS Chi-restraints excluded: chain D residue 31 THR 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 257 LEU Chi-restraints excluded: chain D residue 276 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 236 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** B 63 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3707 r_free = 0.3707 target = 0.144327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115338 restraints weight = 31177.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116172 restraints weight = 31540.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117358 restraints weight = 25485.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117774 restraints weight = 21559.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117934 restraints weight = 19925.104| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21734 Z= 0.117 Angle : 0.582 15.089 29574 Z= 0.284 Chirality : 0.044 0.414 3429 Planarity : 0.004 0.083 3725 Dihedral : 7.108 102.957 3859 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 3.25 % Allowed : 21.37 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2600 helix: 1.49 (0.17), residues: 943 sheet: -1.18 (0.25), residues: 416 loop : -1.44 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 209 TYR 0.019 0.001 TYR D 675 PHE 0.012 0.001 PHE A 458 TRP 0.008 0.001 TRP A 792 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00267 (21673) covalent geometry : angle 0.54654 (29406) SS BOND : bond 0.00275 ( 12) SS BOND : angle 0.84347 ( 24) hydrogen bonds : bond 0.03164 ( 822) hydrogen bonds : angle 4.95934 ( 2376) Misc. bond : bond 0.00071 ( 1) link_ALPHA1-4 : bond 0.00329 ( 1) link_ALPHA1-4 : angle 2.39157 ( 3) link_BETA1-4 : bond 0.00558 ( 17) link_BETA1-4 : angle 1.40979 ( 51) link_NAG-ASN : bond 0.00418 ( 30) link_NAG-ASN : angle 3.51847 ( 90) *********************** 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: 73 poor density : 195 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6150 (mm) REVERT: A 67 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7200 (m90) REVERT: A 166 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7640 (tt) REVERT: A 209 MET cc_start: 0.7386 (tpp) cc_final: 0.7074 (mtt) REVERT: A 354 MET cc_start: 0.7743 (mmm) cc_final: 0.7264 (mmm) REVERT: A 667 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8214 (pp) REVERT: A 755 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7226 (mmm160) REVERT: B 108 LEU cc_start: 0.8849 (mm) cc_final: 0.8331 (mm) REVERT: C 209 MET cc_start: 0.7459 (mmm) cc_final: 0.6899 (mmt) REVERT: C 492 ASN cc_start: 0.3023 (OUTLIER) cc_final: 0.2337 (p0) REVERT: C 795 TYR cc_start: 0.6740 (m-80) cc_final: 0.6423 (m-80) REVERT: D 675 TYR cc_start: 0.5583 (OUTLIER) cc_final: 0.4592 (m-80) REVERT: D 678 PHE cc_start: 0.5061 (OUTLIER) cc_final: 0.4682 (t80) REVERT: D 723 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6844 (tp) outliers start: 73 outliers final: 53 residues processed: 251 average time/residue: 0.1236 time to fit residues: 50.5628 Evaluate side-chains 245 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 314 ILE Chi-restraints excluded: chain A residue 317 THR 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 745 ASP Chi-restraints excluded: chain A residue 747 VAL 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 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 788 LYS 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 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 90 VAL Chi-restraints excluded: chain D residue 180 GLU 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 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 723 LEU 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 5 optimal weight: 0.0970 chunk 223 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 148 optimal weight: 0.0010 chunk 227 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 90 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 overall best weight: 0.3862 ------------------------------------------------------------------------------- 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** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3721 r_free = 0.3721 target = 0.145572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116366 restraints weight = 31170.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117260 restraints weight = 29904.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118646 restraints weight = 24002.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118774 restraints weight = 20284.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120643 restraints weight = 18673.991| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.002 0.065 21734 Z= 0.101 Angle : 0.562 11.243 29574 Z= 0.275 Chirality : 0.044 0.400 3429 Planarity : 0.004 0.083 3725 Dihedral : 6.623 98.974 3859 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 3.03 % Allowed : 21.55 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2600 helix: 1.54 (0.17), residues: 945 sheet: -1.13 (0.25), residues: 416 loop : -1.39 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 209 TYR 0.020 0.001 TYR D 675 PHE 0.013 0.001 PHE A 529 TRP 0.008 0.001 TRP C 768 HIS 0.005 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00220 (21673) covalent geometry : angle 0.53376 (29406) SS BOND : bond 0.00251 ( 12) SS BOND : angle 0.76367 ( 24) hydrogen bonds : bond 0.02954 ( 822) hydrogen bonds : angle 4.86954 ( 2376) Misc. bond : bond 0.00397 ( 1) link_ALPHA1-4 : bond 0.00332 ( 1) link_ALPHA1-4 : angle 2.54973 ( 3) link_BETA1-4 : bond 0.00525 ( 17) link_BETA1-4 : angle 1.24049 ( 51) link_NAG-ASN : bond 0.00390 ( 30) link_NAG-ASN : angle 3.06803 ( 90) *********************** 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 264 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 196 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6085 (mm) REVERT: A 67 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7419 (m90) REVERT: A 209 MET cc_start: 0.7339 (tpp) cc_final: 0.6984 (mtt) REVERT: A 354 MET cc_start: 0.7636 (mmm) cc_final: 0.7182 (mmm) REVERT: A 667 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8212 (pp) REVERT: A 755 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7964 (mtt-85) REVERT: B 101 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7240 (p) REVERT: B 108 LEU cc_start: 0.8822 (mm) cc_final: 0.8295 (mm) REVERT: B 718 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6555 (tt) REVERT: C 492 ASN cc_start: 0.3005 (OUTLIER) cc_final: 0.2326 (p0) REVERT: D 371 MET cc_start: 0.8111 (ttp) cc_final: 0.7805 (ttp) REVERT: D 675 TYR cc_start: 0.5552 (OUTLIER) cc_final: 0.4552 (m-80) REVERT: D 678 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4678 (t80) REVERT: D 723 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6710 (tp) outliers start: 68 outliers final: 44 residues processed: 247 average time/residue: 0.1245 time to fit residues: 49.9011 Evaluate side-chains 237 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 141 VAL 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 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 475 LEU Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 166 LEU 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 338 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** B 91 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115680 restraints weight = 31104.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117338 restraints weight = 30467.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118097 restraints weight = 23484.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118615 restraints weight = 19974.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118684 restraints weight = 18990.999| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1683 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= 0.120 Angle : 0.567 13.334 29574 Z= 0.279 Chirality : 0.044 0.397 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.352 95.890 3859 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 2.94 % Allowed : 21.73 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2600 helix: 1.55 (0.17), residues: 943 sheet: -1.21 (0.25), residues: 426 loop : -1.36 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 209 TYR 0.020 0.001 TYR D 675 PHE 0.011 0.001 PHE C 458 TRP 0.007 0.001 TRP C 381 HIS 0.004 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00278 (21673) covalent geometry : angle 0.53969 (29406) SS BOND : bond 0.00265 ( 12) SS BOND : angle 0.81599 ( 24) hydrogen bonds : bond 0.03067 ( 822) hydrogen bonds : angle 4.87097 ( 2376) Misc. bond : bond 0.00234 ( 1) link_ALPHA1-4 : bond 0.00317 ( 1) link_ALPHA1-4 : angle 2.57254 ( 3) link_BETA1-4 : bond 0.00464 ( 17) link_BETA1-4 : angle 1.20045 ( 51) link_NAG-ASN : bond 0.00382 ( 30) link_NAG-ASN : angle 3.05707 ( 90) *********************** 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 251 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6132 (mm) REVERT: A 67 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7402 (m90) REVERT: A 166 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7620 (tt) REVERT: A 209 MET cc_start: 0.7343 (tpp) cc_final: 0.6959 (mtt) REVERT: A 354 MET cc_start: 0.7657 (mmm) cc_final: 0.7203 (mmm) REVERT: A 667 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 755 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7205 (mmm160) REVERT: B 108 LEU cc_start: 0.8812 (mm) cc_final: 0.8315 (mm) REVERT: B 678 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5922 (t80) REVERT: B 718 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6584 (tt) REVERT: C 209 MET cc_start: 0.7349 (mmm) cc_final: 0.6811 (mmt) REVERT: C 492 ASN cc_start: 0.2943 (OUTLIER) cc_final: 0.2302 (p0) REVERT: C 795 TYR cc_start: 0.6722 (m-10) cc_final: 0.6413 (m-80) REVERT: D 675 TYR cc_start: 0.5580 (OUTLIER) cc_final: 0.4614 (m-80) REVERT: D 678 PHE cc_start: 0.5082 (OUTLIER) cc_final: 0.4723 (t80) REVERT: D 723 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6772 (tp) outliers start: 66 outliers final: 48 residues processed: 233 average time/residue: 0.1285 time to fit residues: 48.3582 Evaluate side-chains 239 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 317 THR 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 276 VAL Chi-restraints excluded: chain B residue 335 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 718 LEU 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 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 99 VAL 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 3 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111530 restraints weight = 31109.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112529 restraints weight = 29233.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113560 restraints weight = 24011.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113904 restraints weight = 20530.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114284 restraints weight = 18879.677| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21734 Z= 0.175 Angle : 0.611 11.502 29574 Z= 0.302 Chirality : 0.046 0.405 3429 Planarity : 0.004 0.081 3725 Dihedral : 6.417 94.436 3859 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 3.03 % Allowed : 21.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2600 helix: 1.40 (0.17), residues: 943 sheet: -1.33 (0.24), residues: 433 loop : -1.38 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 36 TYR 0.020 0.001 TYR D 675 PHE 0.014 0.002 PHE C 197 TRP 0.009 0.001 TRP B 375 HIS 0.008 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00420 (21673) covalent geometry : angle 0.58604 (29406) SS BOND : bond 0.00315 ( 12) SS BOND : angle 0.95224 ( 24) hydrogen bonds : bond 0.03475 ( 822) hydrogen bonds : angle 4.97080 ( 2376) Misc. bond : bond 0.00157 ( 1) link_ALPHA1-4 : bond 0.00336 ( 1) link_ALPHA1-4 : angle 2.50799 ( 3) link_BETA1-4 : bond 0.00469 ( 17) link_BETA1-4 : angle 1.23999 ( 51) link_NAG-ASN : bond 0.00408 ( 30) link_NAG-ASN : angle 3.04952 ( 90) *********************** 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 249 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6251 (mm) REVERT: A 67 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7793 (m170) REVERT: A 166 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 209 MET cc_start: 0.7447 (tpp) cc_final: 0.7076 (mtt) REVERT: A 354 MET cc_start: 0.7680 (mmm) cc_final: 0.7193 (mmm) REVERT: A 667 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (pp) REVERT: A 755 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7257 (mmm160) REVERT: B 108 LEU cc_start: 0.8826 (mm) cc_final: 0.8330 (mm) REVERT: B 678 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.6039 (t80) REVERT: B 718 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6553 (tt) REVERT: C 209 MET cc_start: 0.7444 (mmm) cc_final: 0.6898 (mmt) REVERT: C 254 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8037 (pt) REVERT: C 492 ASN cc_start: 0.3039 (OUTLIER) cc_final: 0.2381 (p0) REVERT: C 795 TYR cc_start: 0.6764 (m-10) cc_final: 0.6489 (m-80) REVERT: D 675 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.4399 (m-80) REVERT: D 678 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4784 (t80) outliers start: 68 outliers final: 53 residues processed: 236 average time/residue: 0.1297 time to fit residues: 49.4858 Evaluate side-chains 233 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 169 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 166 LEU 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 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 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 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 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 718 LEU Chi-restraints excluded: chain B residue 788 LYS 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 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 343 ASP Chi-restraints excluded: chain C residue 354 MET 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 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 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 110 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 238 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 205 optimal weight: 0.0770 chunk 130 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3696 r_free = 0.3696 target = 0.143308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113284 restraints weight = 31127.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114680 restraints weight = 22599.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115664 restraints weight = 19771.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116106 restraints weight = 17800.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116252 restraints weight = 16820.621| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21734 Z= 0.112 Angle : 0.567 12.771 29574 Z= 0.279 Chirality : 0.044 0.395 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.042 90.785 3859 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 2.67 % Allowed : 21.99 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2600 helix: 1.51 (0.17), residues: 944 sheet: -1.25 (0.24), residues: 426 loop : -1.40 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 36 TYR 0.020 0.001 TYR D 675 PHE 0.012 0.001 PHE A 458 TRP 0.009 0.001 TRP C 768 HIS 0.005 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00254 (21673) covalent geometry : angle 0.54373 (29406) SS BOND : bond 0.00276 ( 12) SS BOND : angle 0.80091 ( 24) hydrogen bonds : bond 0.03058 ( 822) hydrogen bonds : angle 4.86937 ( 2376) Misc. bond : bond 0.00141 ( 1) link_ALPHA1-4 : bond 0.00410 ( 1) link_ALPHA1-4 : angle 2.60208 ( 3) link_BETA1-4 : bond 0.00464 ( 17) link_BETA1-4 : angle 1.13005 ( 51) link_NAG-ASN : bond 0.00375 ( 30) link_NAG-ASN : angle 2.79663 ( 90) ********************** 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: 60 poor density : 187 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 67 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7595 (m90) REVERT: A 209 MET cc_start: 0.7400 (tpp) cc_final: 0.7121 (mtt) REVERT: A 354 MET cc_start: 0.7699 (mmm) cc_final: 0.7212 (mmm) REVERT: A 667 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (pp) REVERT: A 755 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7170 (mmm160) REVERT: B 108 LEU cc_start: 0.8842 (mm) cc_final: 0.8337 (mm) REVERT: B 678 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.6005 (t80) REVERT: C 492 ASN cc_start: 0.3179 (OUTLIER) cc_final: 0.2506 (p0) REVERT: C 795 TYR cc_start: 0.6646 (m-10) cc_final: 0.6394 (m-80) REVERT: D 675 TYR cc_start: 0.5266 (OUTLIER) cc_final: 0.4303 (m-80) REVERT: D 678 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4691 (t80) REVERT: D 774 ASP cc_start: 0.7431 (m-30) cc_final: 0.7127 (m-30) outliers start: 60 outliers final: 47 residues processed: 233 average time/residue: 0.1301 time to fit residues: 49.2211 Evaluate side-chains 230 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 317 THR 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 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 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 678 PHE Chi-restraints excluded: chain B residue 788 LYS 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 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 343 ASP Chi-restraints excluded: chain C residue 354 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 C residue 709 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 63 optimal weight: 0.5980 chunk 110 optimal weight: 0.3980 chunk 116 optimal weight: 0.0570 chunk 79 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113557 restraints weight = 31029.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115613 restraints weight = 23762.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116444 restraints weight = 19649.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116710 restraints weight = 17171.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116826 restraints weight = 16790.243| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21734 Z= 0.107 Angle : 0.564 10.660 29574 Z= 0.278 Chirality : 0.043 0.387 3429 Planarity : 0.004 0.082 3725 Dihedral : 5.855 87.296 3859 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 2.40 % Allowed : 22.40 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2600 helix: 1.52 (0.17), residues: 945 sheet: -1.22 (0.25), residues: 425 loop : -1.36 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 434 TYR 0.020 0.001 TYR D 675 PHE 0.011 0.001 PHE A 458 TRP 0.008 0.001 TRP C 381 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00243 (21673) covalent geometry : angle 0.54162 (29406) SS BOND : bond 0.00322 ( 12) SS BOND : angle 1.34182 ( 24) hydrogen bonds : bond 0.03001 ( 822) hydrogen bonds : angle 4.84494 ( 2376) Misc. bond : bond 0.00134 ( 1) link_ALPHA1-4 : bond 0.00354 ( 1) link_ALPHA1-4 : angle 2.43723 ( 3) link_BETA1-4 : bond 0.00446 ( 17) link_BETA1-4 : angle 1.09793 ( 51) link_NAG-ASN : bond 0.00365 ( 30) link_NAG-ASN : angle 2.67157 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.46 seconds wall clock time: 47 minutes 14.72 seconds (2834.72 seconds total)