Starting phenix.real_space_refine on Sun Sep 29 04:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/09_2024/7yfg_33789_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/09_2024/7yfg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/09_2024/7yfg_33789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/09_2024/7yfg_33789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/09_2024/7yfg_33789_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/09_2024/7yfg_33789_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 13413 2.51 5 N 3656 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21215 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5185 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 29, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5045 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 Chain: "C" Number of atoms: 5238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5238 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 30, 'TRANS': 628} Chain breaks: 1 Chain: "D" Number of atoms: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5048 Classifications: {'peptide': 652} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.49, per 1000 atoms: 0.54 Number of scatterers: 21215 At special positions: 0 Unit cell: (122.094, 149.94, 133.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 4048 8.00 N 3656 7.00 C 13413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.04 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG H 2 " - " MAN H 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG S 1 " - " NAG S 2 " " NAG X 1 " - " NAG X 2 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG k 1 " - " NAG k 2 " " NAG n 1 " - " NAG n 2 " " NAG q 1 " - " NAG q 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 901 " - " ASN A 300 " " NAG A 902 " - " ASN A 491 " " NAG A 903 " - " ASN A 440 " " NAG B 901 " - " ASN B 685 " " NAG B 902 " - " ASN B 70 " " NAG B 903 " - " ASN B 438 " " NAG C 901 " - " ASN C 300 " " NAG C 902 " - " ASN C 350 " " NAG C 903 " - " ASN C 491 " " NAG C 904 " - " ASN C 440 " " NAG D 901 " - " ASN D 685 " " NAG D 902 " - " ASN D 70 " " NAG D 903 " - " ASN D 438 " " NAG E 1 " - " ASN A 276 " " NAG G 1 " - " ASN A 771 " " NAG H 1 " - " ASN A 368 " " NAG J 1 " - " ASN A 350 " " NAG K 1 " - " ASN A 61 " " NAG M 1 " - " ASN A 203 " " NAG O 1 " - " ASN A 239 " " NAG S 1 " - " ASN A 471 " " NAG X 1 " - " ASN B 337 " " NAG a 1 " - " ASN C 61 " " NAG c 1 " - " ASN C 203 " " NAG e 1 " - " ASN C 239 " " NAG g 1 " - " ASN C 276 " " NAG k 1 " - " ASN C 771 " " NAG n 1 " - " ASN C 471 " " NAG q 1 " - " ASN C 368 " " NAG v 1 " - " ASN D 337 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 3.0 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: 2.85 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: 8.34 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.21: 8 1.21 - 1.51: 13639 1.51 - 1.82: 8024 1.82 - 2.12: 1 2.12 - 2.42: 1 Bond restraints: 21673 Sorted by residual: bond pdb=" N PRO C 670 " pdb=" CD PRO C 670 " ideal model delta sigma weight residual 1.473 0.942 0.531 1.40e-02 5.10e+03 1.44e+03 bond pdb=" CB PRO D 676 " pdb=" CG PRO D 676 " ideal model delta sigma weight residual 1.492 2.421 -0.929 5.00e-02 4.00e+02 3.45e+02 bond pdb=" CG PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 1.503 0.907 0.596 3.40e-02 8.65e+02 3.07e+02 bond pdb=" CB PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 1.492 0.965 0.527 5.00e-02 4.00e+02 1.11e+02 bond pdb=" CG PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 1.503 1.145 0.358 3.40e-02 8.65e+02 1.11e+02 ... (remaining 21668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 29397 21.22 - 42.44: 7 42.44 - 63.66: 1 63.66 - 84.88: 0 84.88 - 106.09: 1 Bond angle restraints: 29406 Sorted by residual: angle pdb=" CB PRO D 676 " pdb=" CG PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO B 59 " pdb=" CD PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 103.20 73.25 29.95 1.50e+00 4.44e-01 3.99e+02 angle pdb=" CA PRO B 59 " pdb=" CB PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 104.50 68.69 35.81 1.90e+00 2.77e-01 3.55e+02 angle pdb=" N PRO A 304 " pdb=" CD PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 103.20 76.00 27.20 1.50e+00 4.44e-01 3.29e+02 angle pdb=" CA PRO D 676 " pdb=" N PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 112.00 87.87 24.13 1.40e+00 5.10e-01 2.97e+02 ... (remaining 29401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 12494 24.40 - 48.81: 935 48.81 - 73.21: 141 73.21 - 97.62: 54 97.62 - 122.02: 11 Dihedral angle restraints: 13635 sinusoidal: 6094 harmonic: 7541 Sorted by residual: dihedral pdb=" CA GLU C 299 " pdb=" C GLU C 299 " pdb=" N ASN C 300 " pdb=" CA ASN C 300 " ideal model delta harmonic sigma weight residual 180.00 -142.51 -37.49 0 5.00e+00 4.00e-02 5.62e+01 dihedral pdb=" CB CYS D 82 " pdb=" SG CYS D 82 " pdb=" SG CYS D 317 " pdb=" CB CYS D 317 " ideal model delta sinusoidal sigma weight residual 93.00 150.30 -57.30 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" N PRO B 59 " pdb=" CG PRO B 59 " pdb=" CD PRO B 59 " pdb=" CB PRO B 59 " ideal model delta sinusoidal sigma weight residual 30.00 108.98 -78.98 1 1.50e+01 4.44e-03 3.45e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3354 0.120 - 0.239: 66 0.239 - 0.359: 4 0.359 - 0.479: 1 0.479 - 0.599: 4 Chirality restraints: 3429 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.88e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.15e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.60 2.00e-01 2.50e+01 8.96e+00 ... (remaining 3426 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 239 " -0.344 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" CG ASN A 239 " 0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN A 239 " 0.096 2.00e-02 2.50e+03 pdb=" ND2 ASN A 239 " 0.484 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 904 " -0.318 2.00e-02 2.50e+03 2.67e-01 8.91e+02 pdb=" C7 NAG C 904 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 904 " -0.190 2.00e-02 2.50e+03 pdb=" N2 NAG C 904 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG C 904 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.86e+02 pdb=" C7 NAG O 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.047 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 216 2.61 - 3.18: 18438 3.18 - 3.75: 31888 3.75 - 4.33: 43390 4.33 - 4.90: 73031 Nonbonded interactions: 166963 Sorted by model distance: nonbonded pdb=" O ARG A 36 " pdb=" NH1 ARG A 36 " model vdw 2.035 3.120 nonbonded pdb=" OD1 ASN C 300 " pdb=" C1 NAG C 901 " model vdw 2.045 2.776 nonbonded pdb=" OE1 GLU B 410 " pdb=" OG SER B 509 " model vdw 2.054 3.040 nonbonded pdb=" O THR D 791 " pdb=" OG SER D 795 " model vdw 2.125 3.040 nonbonded pdb=" OD2 ASP C 732 " pdb=" N GLY C 905 " model vdw 2.155 3.120 ... (remaining 166958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 25 through 545 or resid 663 through 794 or resid 902 throu \ gh 905)) } ncs_group { reference = (chain 'B' and (resid 29 through 537 or resid 658 through 799 or resid 901 throu \ gh 904)) selection = (chain 'D' and (resid 29 through 799 or resid 901 through 904)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'k' selection = chain 'n' selection = chain 'q' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 47.460 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.140 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- 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 : 0.011 0.929 21673 Z= 0.656 Angle : 1.142 106.094 29406 Z= 0.556 Chirality : 0.052 0.599 3429 Planarity : 0.010 0.267 3725 Dihedral : 17.446 122.025 8751 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.92 % Rotamer: Outliers : 0.22 % Allowed : 21.19 % Favored : 78.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2600 helix: 1.11 (0.17), residues: 924 sheet: -1.26 (0.24), residues: 444 loop : -1.78 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 381 HIS 0.008 0.001 HIS C 371 PHE 0.012 0.001 PHE C 197 TYR 0.033 0.001 TYR D 675 ARG 0.022 0.001 ARG B 209 *********************** 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 fitting. rotamer outliers: 5 poor density : 192 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 443 SER cc_start: 0.3218 (OUTLIER) cc_final: 0.3009 (t) REVERT: D 371 MET cc_start: 0.8435 (tmm) cc_final: 0.7660 (ttp) outliers start: 5 outliers final: 1 residues processed: 197 average time/residue: 0.3321 time to fit residues: 101.8130 Evaluate side-chains 185 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 21673 Z= 0.244 Angle : 0.624 13.705 29406 Z= 0.315 Chirality : 0.046 0.446 3429 Planarity : 0.005 0.091 3725 Dihedral : 9.779 111.057 3862 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 3.43 % Allowed : 19.50 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2600 helix: 1.27 (0.17), residues: 939 sheet: -1.33 (0.24), residues: 424 loop : -1.67 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 281 HIS 0.005 0.001 HIS D 301 PHE 0.012 0.001 PHE A 458 TYR 0.017 0.001 TYR D 675 ARG 0.005 0.000 ARG A 36 *********************** 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 275 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 198 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.6931 (mm) cc_final: 0.6724 (mm) REVERT: A 67 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7747 (m90) REVERT: A 166 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7629 (tt) REVERT: A 354 MET cc_start: 0.7785 (mmm) cc_final: 0.7353 (mmm) REVERT: A 667 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8392 (pp) REVERT: A 755 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7959 (mtt-85) REVERT: B 108 LEU cc_start: 0.8833 (mm) cc_final: 0.8349 (mm) REVERT: B 171 LEU cc_start: 0.7893 (mt) cc_final: 0.7671 (tp) REVERT: B 416 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8495 (m) REVERT: C 209 MET cc_start: 0.7263 (mmm) cc_final: 0.6816 (mmt) REVERT: C 795 TYR cc_start: 0.6708 (m-10) cc_final: 0.6505 (m-80) REVERT: D 371 MET cc_start: 0.8442 (tmm) cc_final: 0.7838 (ttp) outliers start: 77 outliers final: 41 residues processed: 259 average time/residue: 0.3066 time to fit residues: 124.9554 Evaluate side-chains 226 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 180 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 755 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 416 VAL 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 131 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 196 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 236 optimal weight: 0.4980 chunk 255 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21673 Z= 0.172 Angle : 0.550 7.245 29406 Z= 0.280 Chirality : 0.044 0.429 3429 Planarity : 0.004 0.083 3725 Dihedral : 8.760 109.300 3861 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 2.58 % Allowed : 20.35 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2600 helix: 1.37 (0.17), residues: 946 sheet: -1.23 (0.24), residues: 422 loop : -1.54 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.007 0.001 HIS A 53 PHE 0.015 0.001 PHE A 458 TYR 0.024 0.001 TYR D 675 ARG 0.004 0.000 ARG D 194 *********************** 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 254 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 196 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7515 (m90) REVERT: A 166 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7665 (tt) REVERT: A 354 MET cc_start: 0.7783 (mmm) cc_final: 0.7357 (mmm) REVERT: A 667 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8343 (pp) REVERT: A 755 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7918 (mtt-85) REVERT: B 108 LEU cc_start: 0.8813 (mm) cc_final: 0.8343 (mm) REVERT: C 209 MET cc_start: 0.7248 (mmm) cc_final: 0.6818 (mmt) REVERT: C 371 HIS cc_start: 0.7301 (m-70) cc_final: 0.7048 (m170) REVERT: D 371 MET cc_start: 0.8178 (tmm) cc_final: 0.7932 (ttp) outliers start: 58 outliers final: 32 residues processed: 241 average time/residue: 0.3157 time to fit residues: 119.6455 Evaluate side-chains 224 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 257 LEU 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 233 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21673 Z= 0.207 Angle : 0.555 7.533 29406 Z= 0.281 Chirality : 0.045 0.425 3429 Planarity : 0.004 0.083 3725 Dihedral : 8.107 107.594 3859 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 3.43 % Allowed : 20.44 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2600 helix: 1.41 (0.17), residues: 945 sheet: -1.21 (0.24), residues: 422 loop : -1.50 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.005 0.001 HIS A 53 PHE 0.012 0.001 PHE A 458 TYR 0.019 0.001 TYR D 675 ARG 0.004 0.000 ARG D 194 *********************** 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 275 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 198 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7500 (m90) REVERT: A 166 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7653 (tt) REVERT: A 209 MET cc_start: 0.7436 (tpp) cc_final: 0.7127 (mtt) REVERT: A 345 ASP cc_start: 0.6394 (m-30) cc_final: 0.6186 (m-30) REVERT: A 354 MET cc_start: 0.7781 (mmm) cc_final: 0.7334 (mmm) REVERT: A 667 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8339 (pp) REVERT: B 108 LEU cc_start: 0.8842 (mm) cc_final: 0.8315 (mm) REVERT: C 209 MET cc_start: 0.7333 (mmm) cc_final: 0.6897 (mmt) REVERT: C 371 HIS cc_start: 0.7325 (m-70) cc_final: 0.7110 (m-70) REVERT: C 492 ASN cc_start: 0.3208 (OUTLIER) cc_final: 0.2510 (p0) REVERT: D 371 MET cc_start: 0.8230 (tmm) cc_final: 0.8001 (ttp) REVERT: D 675 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.4546 (m-80) REVERT: D 678 PHE cc_start: 0.5212 (OUTLIER) cc_final: 0.4755 (t80) outliers start: 77 outliers final: 51 residues processed: 259 average time/residue: 0.3035 time to fit residues: 124.4655 Evaluate side-chains 240 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 183 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 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 53 HIS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 688 SER 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 209 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 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** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21673 Z= 0.177 Angle : 0.545 8.132 29406 Z= 0.276 Chirality : 0.044 0.419 3429 Planarity : 0.004 0.083 3725 Dihedral : 7.492 105.494 3859 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 3.43 % Allowed : 20.79 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2600 helix: 1.48 (0.17), residues: 944 sheet: -1.16 (0.24), residues: 422 loop : -1.46 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A 53 PHE 0.012 0.001 PHE A 458 TYR 0.019 0.001 TYR D 675 ARG 0.005 0.000 ARG B 209 *********************** 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 275 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 198 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6272 (mm) REVERT: A 67 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7333 (m90) REVERT: A 166 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 209 MET cc_start: 0.7386 (tpp) cc_final: 0.7057 (mtt) REVERT: A 354 MET cc_start: 0.7754 (mmm) cc_final: 0.7302 (mmm) REVERT: A 667 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8314 (pp) REVERT: A 755 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7189 (mmm160) REVERT: B 108 LEU cc_start: 0.8817 (mm) cc_final: 0.8306 (mm) REVERT: C 370 THR cc_start: 0.8046 (m) cc_final: 0.7845 (p) REVERT: C 795 TYR cc_start: 0.6676 (m-80) cc_final: 0.6396 (m-80) REVERT: D 371 MET cc_start: 0.8222 (tmm) cc_final: 0.7968 (ttp) REVERT: D 675 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.4544 (m-80) REVERT: D 678 PHE cc_start: 0.5227 (OUTLIER) cc_final: 0.4843 (t80) outliers start: 77 outliers final: 50 residues processed: 260 average time/residue: 0.2870 time to fit residues: 119.7587 Evaluate side-chains 241 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 184 time to evaluate : 2.530 ------------------------------------------------------------------------------- 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 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 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 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 475 LEU Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain 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 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 84 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** C 709 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21673 Z= 0.352 Angle : 0.633 9.471 29406 Z= 0.321 Chirality : 0.048 0.435 3429 Planarity : 0.005 0.081 3725 Dihedral : 7.592 104.813 3859 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 4.01 % Allowed : 21.02 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2600 helix: 1.27 (0.17), residues: 943 sheet: -1.41 (0.24), residues: 423 loop : -1.51 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 375 HIS 0.013 0.001 HIS A 67 PHE 0.019 0.002 PHE C 197 TYR 0.019 0.002 TYR D 675 ARG 0.004 0.000 ARG C 36 *********************** 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 274 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 184 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6423 (mm) REVERT: A 67 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7042 (m90) REVERT: A 166 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7673 (tt) REVERT: A 354 MET cc_start: 0.7789 (mmm) cc_final: 0.7327 (mmm) REVERT: A 667 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8356 (pp) REVERT: A 755 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7271 (mmm160) REVERT: B 108 LEU cc_start: 0.8874 (mm) cc_final: 0.8320 (mm) REVERT: B 171 LEU cc_start: 0.7480 (tp) cc_final: 0.7233 (tp) REVERT: B 678 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.6109 (t80) REVERT: C 209 MET cc_start: 0.7382 (mmm) cc_final: 0.6854 (mmt) REVERT: C 492 ASN cc_start: 0.3178 (OUTLIER) cc_final: 0.2459 (p0) REVERT: D 371 MET cc_start: 0.8312 (tmm) cc_final: 0.7953 (ttt) REVERT: D 675 TYR cc_start: 0.5519 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: D 678 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.5114 (t80) outliers start: 90 outliers final: 63 residues processed: 256 average time/residue: 0.3044 time to fit residues: 124.9259 Evaluate side-chains 244 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 172 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 58 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 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 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 440 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 678 PHE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 87 VAL 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 324 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 143 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 211 optimal weight: 0.0270 chunk 140 optimal weight: 0.5980 chunk 250 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21673 Z= 0.154 Angle : 0.547 8.683 29406 Z= 0.278 Chirality : 0.044 0.416 3429 Planarity : 0.004 0.083 3725 Dihedral : 6.884 100.533 3859 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 2.67 % Allowed : 22.04 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2600 helix: 1.45 (0.17), residues: 943 sheet: -1.27 (0.25), residues: 416 loop : -1.45 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 792 HIS 0.004 0.001 HIS A 67 PHE 0.014 0.001 PHE A 458 TYR 0.020 0.001 TYR D 675 ARG 0.005 0.000 ARG B 209 *********************** 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 248 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 188 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6215 (mm) REVERT: A 67 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7550 (m90) REVERT: A 354 MET cc_start: 0.7748 (mmm) cc_final: 0.7296 (mmm) REVERT: A 667 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 108 LEU cc_start: 0.8808 (mm) cc_final: 0.8308 (mm) REVERT: B 718 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6689 (tt) REVERT: C 254 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7881 (pt) REVERT: C 492 ASN cc_start: 0.3172 (OUTLIER) cc_final: 0.2466 (p0) REVERT: D 371 MET cc_start: 0.8242 (tmm) cc_final: 0.7852 (ttt) REVERT: D 675 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.4540 (m-80) REVERT: D 678 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.5101 (t80) REVERT: D 723 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6895 (tp) REVERT: D 774 ASP cc_start: 0.7259 (m-30) cc_final: 0.6973 (m-30) outliers start: 60 outliers final: 36 residues processed: 235 average time/residue: 0.2966 time to fit residues: 115.0722 Evaluate side-chains 223 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 2.299 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 295 LEU 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 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 718 LEU 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 182 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 276 VAL 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 155 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 196 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21673 Z= 0.236 Angle : 0.578 12.682 29406 Z= 0.290 Chirality : 0.045 0.410 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.727 98.359 3859 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 2.89 % Allowed : 21.86 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2600 helix: 1.42 (0.17), residues: 943 sheet: -1.37 (0.24), residues: 433 loop : -1.45 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.006 0.001 HIS A 67 PHE 0.012 0.001 PHE A 458 TYR 0.020 0.001 TYR D 675 ARG 0.005 0.000 ARG B 209 *********************** 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 239 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 174 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6332 (mm) REVERT: A 44 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6768 (mm-30) REVERT: A 67 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7330 (m90) REVERT: A 166 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 354 MET cc_start: 0.7759 (mmm) cc_final: 0.7291 (mmm) REVERT: A 667 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8334 (pp) REVERT: A 755 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7185 (mmm160) REVERT: B 108 LEU cc_start: 0.8813 (mm) cc_final: 0.8264 (mm) REVERT: B 718 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6680 (tt) REVERT: C 209 MET cc_start: 0.7226 (mmm) cc_final: 0.6732 (mmt) REVERT: C 254 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8074 (pt) REVERT: C 492 ASN cc_start: 0.3115 (OUTLIER) cc_final: 0.2398 (p0) REVERT: C 795 TYR cc_start: 0.6693 (m-10) cc_final: 0.6424 (m-80) REVERT: D 371 MET cc_start: 0.8333 (tmm) cc_final: 0.7883 (ttt) REVERT: D 675 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.4573 (m-80) REVERT: D 678 PHE cc_start: 0.5401 (OUTLIER) cc_final: 0.4943 (t80) REVERT: D 723 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6918 (tp) REVERT: D 774 ASP cc_start: 0.7351 (m-30) cc_final: 0.6997 (m-30) outliers start: 65 outliers final: 46 residues processed: 230 average time/residue: 0.2872 time to fit residues: 107.5406 Evaluate side-chains 225 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 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 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 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 718 LEU Chi-restraints excluded: chain B residue 756 THR 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 182 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 276 VAL 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 227 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 233 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 232 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21673 Z= 0.179 Angle : 0.555 9.154 29406 Z= 0.281 Chirality : 0.045 0.521 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.420 95.598 3859 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 2.67 % Allowed : 22.13 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2600 helix: 1.46 (0.17), residues: 943 sheet: -1.32 (0.24), residues: 426 loop : -1.43 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 792 HIS 0.005 0.001 HIS A 709 PHE 0.012 0.001 PHE A 458 TYR 0.021 0.001 TYR D 675 ARG 0.005 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6201 (mm) REVERT: A 44 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6842 (mm-30) REVERT: A 67 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7522 (m90) REVERT: A 166 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7646 (tt) REVERT: A 354 MET cc_start: 0.7749 (mmm) cc_final: 0.7296 (mmm) REVERT: A 667 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 755 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7147 (mmm160) REVERT: B 108 LEU cc_start: 0.8820 (mm) cc_final: 0.8318 (mm) REVERT: B 718 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6712 (tt) REVERT: C 209 MET cc_start: 0.7202 (mmm) cc_final: 0.6701 (mmt) REVERT: C 254 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7902 (pt) REVERT: C 492 ASN cc_start: 0.3075 (OUTLIER) cc_final: 0.2370 (p0) REVERT: C 795 TYR cc_start: 0.6681 (m-10) cc_final: 0.6404 (m-80) REVERT: D 371 MET cc_start: 0.8305 (tmm) cc_final: 0.7821 (ttt) REVERT: D 675 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.4416 (m-80) REVERT: D 678 PHE cc_start: 0.5310 (OUTLIER) cc_final: 0.4884 (t80) REVERT: D 723 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6871 (tp) REVERT: D 774 ASP cc_start: 0.7328 (m-30) cc_final: 0.6999 (m-30) outliers start: 60 outliers final: 43 residues processed: 235 average time/residue: 0.3026 time to fit residues: 113.3658 Evaluate side-chains 226 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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 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 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 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 276 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.5980 chunk 246 optimal weight: 8.9990 chunk 150 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 259 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21673 Z= 0.170 Angle : 0.548 9.694 29406 Z= 0.276 Chirality : 0.043 0.390 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.169 92.949 3859 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 2.72 % Allowed : 21.99 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2600 helix: 1.49 (0.17), residues: 944 sheet: -1.22 (0.25), residues: 414 loop : -1.43 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 281 HIS 0.004 0.001 HIS A 709 PHE 0.011 0.001 PHE A 458 TYR 0.021 0.001 TYR D 675 ARG 0.005 0.000 ARG C 36 ********************** 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 246 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 185 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6176 (mm) REVERT: A 44 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6833 (mm-30) REVERT: A 67 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7464 (m90) REVERT: A 354 MET cc_start: 0.7735 (mmm) cc_final: 0.7286 (mmm) REVERT: A 667 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8309 (pp) REVERT: A 755 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7137 (mmm160) REVERT: B 108 LEU cc_start: 0.8805 (mm) cc_final: 0.8316 (mm) REVERT: C 209 MET cc_start: 0.7237 (mmm) cc_final: 0.6706 (mmt) REVERT: C 492 ASN cc_start: 0.3050 (OUTLIER) cc_final: 0.2364 (p0) REVERT: C 795 TYR cc_start: 0.6560 (m-10) cc_final: 0.6335 (m-80) REVERT: D 371 MET cc_start: 0.8317 (tmm) cc_final: 0.7897 (ttt) REVERT: D 675 TYR cc_start: 0.5290 (OUTLIER) cc_final: 0.4318 (m-80) REVERT: D 678 PHE cc_start: 0.5273 (OUTLIER) cc_final: 0.4851 (t80) REVERT: D 723 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6902 (tp) REVERT: D 774 ASP cc_start: 0.7341 (m-30) cc_final: 0.6978 (m-30) outliers start: 61 outliers final: 47 residues processed: 233 average time/residue: 0.2905 time to fit residues: 109.5066 Evaluate side-chains 234 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 179 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 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 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 359 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.5980 chunk 219 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** 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 = 0.3693 r_free = 0.3693 target = 0.143161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112080 restraints weight = 31087.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114136 restraints weight = 24270.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114941 restraints weight = 20529.421| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 21673 Z= 0.191 Angle : 0.552 9.609 29406 Z= 0.278 Chirality : 0.044 0.385 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.004 90.589 3859 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 2.76 % Allowed : 21.99 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2600 helix: 1.50 (0.17), residues: 944 sheet: -1.21 (0.25), residues: 414 loop : -1.41 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 381 HIS 0.019 0.001 HIS A 67 PHE 0.011 0.001 PHE A 458 TYR 0.020 0.001 TYR D 675 ARG 0.005 0.000 ARG C 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.58 seconds wall clock time: 68 minutes 34.89 seconds (4114.89 seconds total)