Starting phenix.real_space_refine on Sun Feb 18 09:25:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/02_2024/7yfg_33789_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/02_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_33789/02_2024/7yfg_33789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/02_2024/7yfg_33789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/02_2024/7yfg_33789_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/02_2024/7yfg_33789_neut.pdb" } 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 Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 741": "OE1" <-> "OE2" Residue "B GLU 790": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 785": "OE1" <-> "OE2" Residue "D GLU 790": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "D GLU 904": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.19, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 9.64 Conformation dependent library (CDL) restraints added in 4.1 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: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.503A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.031A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.942A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.767A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.985A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.547A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.675A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 744 removed outlier: 3.754A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.546A pdb=" N VAL A 772 " --> pdb=" O TRP A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.567A pdb=" N ARG B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.610A pdb=" N ALA B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.611A pdb=" N GLN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.833A pdb=" N GLN B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.794A pdb=" N ASN B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 696 through 707 removed outlier: 4.226A pdb=" N LYS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE B 706 " --> pdb=" O HIS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 730 through 740 Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 784 through 794 Processing helix chain 'C' and resid 37 through 53 removed outlier: 3.539A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.659A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.834A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.941A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.918A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.594A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.521A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 276 through 296 Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 526 removed outlier: 4.126A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.777A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 724 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.647A pdb=" N LEU D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 removed outlier: 4.225A pdb=" N SER D 126 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 128 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.529A pdb=" N GLN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 188 Processing helix chain 'D' and resid 208 through 217 removed outlier: 4.311A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 284 through 308 Processing helix chain 'D' and resid 325 through 337 removed outlier: 4.082A pdb=" N ASN D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 520 removed outlier: 3.871A pdb=" N ILE D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 696 through 704 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.558A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.637A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 7.858A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.919A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.383A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.556A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.895A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.765A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.319A pdb=" N VAL B 30 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU B 65 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 93 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE B 122 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 95 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.923A pdb=" N PHE B 165 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 198 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B 167 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 200 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 169 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 223 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 276 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 477 removed outlier: 6.928A pdb=" N LEU B 403 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR B 476 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL B 405 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 505 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.948A pdb=" N THR B 450 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.056A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.056A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 527 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY B 758 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 529 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR B 756 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.956A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 32 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.604A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.549A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.626A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 413 removed outlier: 6.184A pdb=" N ILE C 435 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU C 478 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR C 437 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC3, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.010A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.555A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 64 through 66 removed outlier: 6.803A pdb=" N ILE D 93 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 122 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE D 95 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 198 through 200 removed outlier: 8.981A pdb=" N LEU D 199 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 167 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 274 through 278 removed outlier: 6.562A pdb=" N MET D 358 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG D 374 " --> pdb=" O MET D 358 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL D 360 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AC9, first strand: chain 'D' and resid 389 through 390 removed outlier: 4.272A pdb=" N ARG D 389 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 472 through 477 removed outlier: 3.843A pdb=" N VAL D 405 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 415 through 417 Processing sheet with id=AD3, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AD4, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.666A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.666A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 527 " --> pdb=" O GLY D 758 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY D 758 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR D 529 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 756 " --> pdb=" O THR D 529 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.63 Time building geometry restraints manager: 10.24 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: 0.01 - 30.60: 1 30.60 - 61.19: 0 61.19 - 91.78: 9 91.78 - 122.37: 26169 122.37 - 152.96: 3227 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 2.520 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 2.440 nonbonded pdb=" O THR D 791 " pdb=" OG SER D 795 " model vdw 2.125 2.440 nonbonded pdb=" OD2 ASP C 732 " pdb=" N GLY C 905 " model vdw 2.155 2.520 ... (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 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: 1.170 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: 6.380 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 59.010 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.850 ------------------------------------------------------------------------------- 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 : 2.530 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: 0.3369 time to fit residues: 102.6564 Evaluate side-chains 185 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 151 optimal weight: 0.2980 chunk 236 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN C 371 HIS D 43 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 21673 Z= 0.199 Angle : 0.587 13.335 29406 Z= 0.296 Chirality : 0.045 0.436 3429 Planarity : 0.005 0.094 3725 Dihedral : 9.856 111.051 3862 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 2.94 % Allowed : 20.12 % Favored : 76.94 % 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: -0.68 (0.17), residues: 2600 helix: 1.41 (0.17), residues: 938 sheet: -1.29 (0.24), residues: 427 loop : -1.64 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 56 HIS 0.005 0.001 HIS D 301 PHE 0.011 0.001 PHE A 458 TYR 0.014 0.001 TYR D 675 ARG 0.004 0.000 ARG B 209 *********************** 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 263 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 197 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7667 (m90) REVERT: A 166 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7588 (tt) REVERT: A 203 ASN cc_start: 0.3546 (t0) cc_final: 0.3231 (t0) REVERT: A 346 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6503 (ttt90) REVERT: A 354 MET cc_start: 0.7776 (mmm) cc_final: 0.7340 (mmm) REVERT: A 667 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8393 (pp) REVERT: B 108 LEU cc_start: 0.8790 (mm) cc_final: 0.8307 (mm) REVERT: B 171 LEU cc_start: 0.7846 (mt) cc_final: 0.7598 (tp) REVERT: B 409 GLU cc_start: 0.6630 (tt0) cc_final: 0.6260 (tt0) REVERT: C 209 MET cc_start: 0.7128 (mmm) cc_final: 0.6702 (mmt) REVERT: D 371 MET cc_start: 0.8414 (tmm) cc_final: 0.7788 (ttp) outliers start: 66 outliers final: 37 residues processed: 246 average time/residue: 0.3090 time to fit residues: 120.0432 Evaluate side-chains 224 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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 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 346 ARG Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 529 THR 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 372 VAL Chi-restraints excluded: chain C residue 396 THR 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 236 optimal weight: 0.0980 chunk 255 optimal weight: 0.5980 chunk 210 optimal weight: 0.6980 chunk 234 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21673 Z= 0.213 Angle : 0.554 7.197 29406 Z= 0.281 Chirality : 0.045 0.429 3429 Planarity : 0.004 0.083 3725 Dihedral : 8.758 108.776 3861 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 3.16 % Allowed : 20.26 % Favored : 76.58 % 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: -0.62 (0.17), residues: 2600 helix: 1.44 (0.17), residues: 943 sheet: -1.33 (0.24), residues: 428 loop : -1.57 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.006 0.001 HIS A 67 PHE 0.013 0.001 PHE A 458 TYR 0.023 0.001 TYR D 675 ARG 0.004 0.000 ARG B 209 *********************** 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 262 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 191 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7665 (tt) REVERT: A 203 ASN cc_start: 0.3542 (t0) cc_final: 0.3268 (t0) REVERT: A 346 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6448 (ttt90) REVERT: A 354 MET cc_start: 0.7780 (mmm) cc_final: 0.7314 (mmm) REVERT: A 667 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8356 (pp) REVERT: B 108 LEU cc_start: 0.8810 (mm) cc_final: 0.8338 (mm) REVERT: B 171 LEU cc_start: 0.7813 (mt) cc_final: 0.7607 (tp) REVERT: C 209 MET cc_start: 0.7261 (mmm) cc_final: 0.6830 (mmt) REVERT: C 371 HIS cc_start: 0.7328 (m-70) cc_final: 0.7088 (m170) REVERT: C 795 TYR cc_start: 0.6751 (m-10) cc_final: 0.6471 (m-80) REVERT: D 371 MET cc_start: 0.8192 (tmm) cc_final: 0.7922 (ttp) outliers start: 71 outliers final: 45 residues processed: 249 average time/residue: 0.3337 time to fit residues: 130.5655 Evaluate side-chains 230 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 2.529 ------------------------------------------------------------------------------- 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 107 VAL 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 346 ARG 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 685 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 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 529 THR 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 98 ASN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 203 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: 0.9990 chunk 177 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 0.0570 chunk 237 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 702 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21673 Z= 0.199 Angle : 0.542 7.735 29406 Z= 0.274 Chirality : 0.044 0.426 3429 Planarity : 0.004 0.083 3725 Dihedral : 7.846 105.750 3861 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 3.70 % Allowed : 21.10 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.17), residues: 2600 helix: 1.47 (0.17), residues: 944 sheet: -1.27 (0.24), residues: 427 loop : -1.48 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 281 HIS 0.005 0.001 HIS A 67 PHE 0.011 0.001 PHE A 458 TYR 0.019 0.001 TYR D 675 ARG 0.012 0.000 ARG A 187 *********************** 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 281 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 198 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7638 (tt) REVERT: A 203 ASN cc_start: 0.3436 (t0) cc_final: 0.3181 (t0) REVERT: A 346 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6285 (ttt90) REVERT: A 354 MET cc_start: 0.7783 (mmm) cc_final: 0.7321 (mmm) REVERT: A 667 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8346 (pp) REVERT: B 108 LEU cc_start: 0.8823 (mm) cc_final: 0.8336 (mm) REVERT: C 209 MET cc_start: 0.7360 (mmm) cc_final: 0.6914 (mmt) REVERT: C 371 HIS cc_start: 0.7224 (m-70) cc_final: 0.7008 (m170) REVERT: C 795 TYR cc_start: 0.6674 (m-10) cc_final: 0.6447 (m-80) REVERT: D 678 PHE cc_start: 0.5287 (OUTLIER) cc_final: 0.4929 (t80) outliers start: 83 outliers final: 58 residues processed: 262 average time/residue: 0.3182 time to fit residues: 130.4221 Evaluate side-chains 247 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 185 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 132 SER 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 241 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 346 ARG Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP 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 685 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 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 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 529 THR Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 ASP 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 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: 0.7980 chunk 142 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 173 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS ** 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** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1279 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= 0.176 Angle : 0.535 8.322 29406 Z= 0.269 Chirality : 0.044 0.417 3429 Planarity : 0.004 0.082 3725 Dihedral : 7.330 102.621 3859 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.83 % Allowed : 21.50 % Favored : 74.67 % 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: -0.44 (0.17), residues: 2600 helix: 1.54 (0.17), residues: 943 sheet: -1.19 (0.25), residues: 425 loop : -1.43 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A 780 PHE 0.011 0.001 PHE A 458 TYR 0.017 0.001 TYR D 675 ARG 0.007 0.000 ARG D 194 *********************** 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 281 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 195 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6307 (tpt170) cc_final: 0.6084 (tpt90) REVERT: A 166 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7608 (tt) REVERT: A 203 ASN cc_start: 0.3488 (t0) cc_final: 0.3236 (t0) REVERT: A 346 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6439 (ttt90) REVERT: A 354 MET cc_start: 0.7772 (mmm) cc_final: 0.7310 (mmm) REVERT: A 667 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8318 (pp) REVERT: B 108 LEU cc_start: 0.8821 (mm) cc_final: 0.8344 (mm) REVERT: C 795 TYR cc_start: 0.6699 (m-10) cc_final: 0.6488 (m-80) REVERT: D 675 TYR cc_start: 0.5559 (OUTLIER) cc_final: 0.4680 (m-80) outliers start: 86 outliers final: 55 residues processed: 263 average time/residue: 0.3149 time to fit residues: 130.9399 Evaluate side-chains 242 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 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 346 ARG Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP 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 685 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 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 529 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 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 443 SER 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 57 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 675 TYR 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: 0.9990 chunk 49 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 251 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21673 Z= 0.184 Angle : 0.531 8.702 29406 Z= 0.268 Chirality : 0.044 0.408 3429 Planarity : 0.004 0.082 3725 Dihedral : 6.893 97.877 3859 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 3.74 % Allowed : 21.46 % Favored : 74.80 % 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: -0.39 (0.17), residues: 2600 helix: 1.56 (0.17), residues: 943 sheet: -1.15 (0.25), residues: 425 loop : -1.39 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.004 0.001 HIS A 780 PHE 0.012 0.001 PHE C 458 TYR 0.016 0.001 TYR D 675 ARG 0.006 0.000 ARG D 194 *********************** 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 276 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 192 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6338 (tpt170) cc_final: 0.6099 (tpt90) REVERT: A 166 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7590 (tt) REVERT: A 203 ASN cc_start: 0.3473 (t0) cc_final: 0.3184 (t0) REVERT: A 346 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6545 (ttt90) REVERT: A 354 MET cc_start: 0.7686 (mmm) cc_final: 0.7236 (mmm) REVERT: A 667 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8308 (pp) REVERT: B 108 LEU cc_start: 0.8823 (mm) cc_final: 0.8332 (mm) REVERT: C 209 MET cc_start: 0.7228 (mmm) cc_final: 0.6734 (mmt) REVERT: C 795 TYR cc_start: 0.6681 (m-10) cc_final: 0.6466 (m-80) REVERT: D 675 TYR cc_start: 0.5238 (OUTLIER) cc_final: 0.4374 (m-80) REVERT: D 678 PHE cc_start: 0.5296 (OUTLIER) cc_final: 0.4872 (t80) outliers start: 84 outliers final: 62 residues processed: 262 average time/residue: 0.3091 time to fit residues: 129.9474 Evaluate side-chains 255 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 188 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 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 343 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP 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 685 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 756 THR 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 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 443 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 211 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 250 optimal weight: 0.1980 chunk 156 optimal weight: 0.7980 chunk 152 optimal weight: 0.0070 chunk 115 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21673 Z= 0.148 Angle : 0.524 10.574 29406 Z= 0.262 Chirality : 0.043 0.395 3429 Planarity : 0.004 0.083 3725 Dihedral : 6.403 92.062 3859 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 3.29 % Allowed : 21.91 % Favored : 74.80 % 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: -0.30 (0.17), residues: 2600 helix: 1.64 (0.17), residues: 942 sheet: -1.07 (0.25), residues: 424 loop : -1.36 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 769 HIS 0.004 0.001 HIS A 780 PHE 0.011 0.001 PHE A 458 TYR 0.017 0.001 TYR D 675 ARG 0.005 0.000 ARG D 194 *********************** 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 271 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 197 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6261 (tpt170) cc_final: 0.6042 (tpt90) REVERT: A 203 ASN cc_start: 0.3467 (t0) cc_final: 0.3169 (t0) REVERT: A 346 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6580 (ttt90) REVERT: A 354 MET cc_start: 0.7671 (mmm) cc_final: 0.7225 (mmm) REVERT: A 667 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8307 (pp) REVERT: B 108 LEU cc_start: 0.8808 (mm) cc_final: 0.8328 (mm) REVERT: D 675 TYR cc_start: 0.5186 (OUTLIER) cc_final: 0.4374 (m-80) REVERT: D 678 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.4798 (t80) REVERT: D 774 ASP cc_start: 0.7268 (m-30) cc_final: 0.6964 (m-30) outliers start: 74 outliers final: 51 residues processed: 255 average time/residue: 0.3235 time to fit residues: 129.9918 Evaluate side-chains 239 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 184 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 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 529 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 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 373 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 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** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21673 Z= 0.203 Angle : 0.544 9.776 29406 Z= 0.273 Chirality : 0.044 0.396 3429 Planarity : 0.004 0.081 3725 Dihedral : 6.201 86.966 3859 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 3.47 % Allowed : 22.13 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2600 helix: 1.59 (0.17), residues: 944 sheet: -1.12 (0.25), residues: 424 loop : -1.36 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.004 0.001 HIS A 477 PHE 0.012 0.001 PHE C 458 TYR 0.017 0.001 TYR D 675 ARG 0.004 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 260 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 182 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ASN cc_start: 0.3504 (t0) cc_final: 0.3224 (t0) REVERT: A 346 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6673 (ttt90) REVERT: A 354 MET cc_start: 0.7685 (mmm) cc_final: 0.7234 (mmm) REVERT: A 667 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8365 (pp) REVERT: B 108 LEU cc_start: 0.8809 (mm) cc_final: 0.8320 (mm) REVERT: B 718 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6739 (tt) REVERT: C 209 MET cc_start: 0.7200 (mmm) cc_final: 0.6706 (mmt) REVERT: D 675 TYR cc_start: 0.5218 (OUTLIER) cc_final: 0.4326 (m-80) REVERT: D 678 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.4860 (t80) REVERT: D 774 ASP cc_start: 0.7309 (m-30) cc_final: 0.6993 (m-30) outliers start: 78 outliers final: 61 residues processed: 246 average time/residue: 0.2979 time to fit residues: 118.4115 Evaluate side-chains 244 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 178 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 241 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 343 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP 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 685 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 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 529 THR Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 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 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 709 HIS 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 220 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 282 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 140 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 0.0000 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21673 Z= 0.153 Angle : 0.526 10.222 29406 Z= 0.264 Chirality : 0.043 0.385 3429 Planarity : 0.004 0.082 3725 Dihedral : 5.752 78.635 3859 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 3.16 % Allowed : 22.40 % Favored : 74.44 % 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: -0.28 (0.17), residues: 2600 helix: 1.63 (0.17), residues: 944 sheet: -1.04 (0.25), residues: 423 loop : -1.34 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 381 HIS 0.006 0.001 HIS A 709 PHE 0.011 0.001 PHE C 458 TYR 0.017 0.001 TYR D 675 ARG 0.005 0.000 ARG A 187 *********************** 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 261 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 190 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.6281 (tpt90) cc_final: 0.6073 (tpt90) REVERT: A 44 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6874 (mm-30) REVERT: A 203 ASN cc_start: 0.3501 (t0) cc_final: 0.3207 (t0) REVERT: A 346 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6701 (ttt90) REVERT: A 667 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8329 (pp) REVERT: B 108 LEU cc_start: 0.8807 (mm) cc_final: 0.8321 (mm) REVERT: C 209 MET cc_start: 0.7151 (mmm) cc_final: 0.6655 (mmt) REVERT: C 795 TYR cc_start: 0.6602 (m-80) cc_final: 0.6313 (m-80) REVERT: D 675 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.4384 (m-80) REVERT: D 678 PHE cc_start: 0.5275 (OUTLIER) cc_final: 0.4885 (t80) REVERT: D 774 ASP cc_start: 0.7315 (m-30) cc_final: 0.6991 (m-30) outliers start: 71 outliers final: 59 residues processed: 248 average time/residue: 0.2943 time to fit residues: 117.3508 Evaluate side-chains 244 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 181 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP 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 685 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 335 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 529 THR Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 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 664 ILE Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 282 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 chunk 150 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21673 Z= 0.178 Angle : 0.540 10.346 29406 Z= 0.270 Chirality : 0.043 0.385 3429 Planarity : 0.004 0.081 3725 Dihedral : 5.579 77.894 3859 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 3.12 % Allowed : 22.53 % Favored : 74.35 % 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: -0.30 (0.17), residues: 2600 helix: 1.61 (0.17), residues: 944 sheet: -1.05 (0.25), residues: 424 loop : -1.34 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 381 HIS 0.004 0.001 HIS A 709 PHE 0.011 0.001 PHE C 458 TYR 0.018 0.001 TYR D 675 ARG 0.007 0.000 ARG B 434 ********************** 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 255 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 185 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6880 (mm-30) REVERT: A 203 ASN cc_start: 0.3509 (t0) cc_final: 0.3219 (t0) REVERT: A 346 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6743 (ttt90) REVERT: A 667 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8327 (pp) REVERT: B 108 LEU cc_start: 0.8794 (mm) cc_final: 0.8325 (mm) REVERT: B 720 MET cc_start: 0.7071 (mmt) cc_final: 0.6804 (mmt) REVERT: D 675 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.4370 (m-80) REVERT: D 678 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.4824 (t80) REVERT: D 774 ASP cc_start: 0.7347 (m-30) cc_final: 0.7019 (m-30) outliers start: 70 outliers final: 64 residues processed: 241 average time/residue: 0.2987 time to fit residues: 115.9836 Evaluate side-chains 250 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 182 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 481 ASP 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 685 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 335 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 529 THR Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 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 366 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 443 SER 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 98 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 282 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 4.9990 chunk 219 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114026 restraints weight = 30883.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115310 restraints weight = 29061.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115934 restraints weight = 23527.153| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21673 Z= 0.186 Angle : 0.538 9.687 29406 Z= 0.271 Chirality : 0.043 0.383 3429 Planarity : 0.004 0.081 3725 Dihedral : 5.394 77.545 3859 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 3.25 % Allowed : 22.40 % Favored : 74.35 % 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: -0.32 (0.17), residues: 2600 helix: 1.60 (0.17), residues: 943 sheet: -1.06 (0.25), residues: 424 loop : -1.36 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 792 HIS 0.004 0.001 HIS A 780 PHE 0.012 0.001 PHE C 458 TYR 0.018 0.001 TYR D 675 ARG 0.004 0.000 ARG C 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.93 seconds wall clock time: 67 minutes 32.44 seconds (4052.44 seconds total)