Starting phenix.real_space_refine on Sun Feb 18 10:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i91_35254/02_2024/8i91_35254.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i91_35254/02_2024/8i91_35254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i91_35254/02_2024/8i91_35254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i91_35254/02_2024/8i91_35254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i91_35254/02_2024/8i91_35254.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i91_35254/02_2024/8i91_35254.pdb" } resolution = 3.3 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= 0.007 sd= 0.117 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 130 5.16 5 Cl 2 4.86 5 C 14100 2.51 5 N 3486 2.21 5 O 4044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C ARG 518": "NH1" <-> "NH2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "C PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 350": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21764 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "B" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4552 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 557} Chain: "C" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "D" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4552 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 557} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.13, per 1000 atoms: 0.51 Number of scatterers: 21764 At special positions: 0 Unit cell: (122.831, 138.049, 179.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 130 16.00 O 4044 8.00 N 3486 7.00 C 14100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " 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=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B 703 " - " ASN B 131 " " NAG C 901 " - " ASN C 322 " " NAG D 703 " - " ASN D 131 " " NAG E 1 " - " ASN A 53 " " NAG F 1 " - " ASN A 90 " " NAG G 1 " - " ASN A 103 " " NAG H 1 " - " ASN A 432 " " NAG I 1 " - " ASN A 546 " " NAG J 1 " - " ASN A 690 " " NAG K 1 " - " ASN B 357 " " NAG L 1 " - " ASN C 53 " " NAG M 1 " - " ASN C 90 " " NAG N 1 " - " ASN C 103 " " NAG O 1 " - " ASN C 432 " " NAG P 1 " - " ASN C 546 " " NAG Q 1 " - " ASN C 690 " " NAG R 1 " - " ASN D 357 " Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 12 sheets defined 65.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.593A pdb=" N ASP A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.850A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.684A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.992A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.566A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.535A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.591A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.751A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.908A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.614A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.528A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.030A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.699A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.606A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.729A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.630A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.816A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.648A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.988A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.593A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.313A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.520A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.818A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.612A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.517A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.565A pdb=" N VAL A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 removed outlier: 3.513A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.971A pdb=" N VAL B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.203A pdb=" N VAL B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.640A pdb=" N TYR B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.622A pdb=" N LEU B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.688A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.635A pdb=" N THR B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 85 through 116 removed outlier: 4.203A pdb=" N VAL B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.613A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 168 through 185 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 192 through 202 removed outlier: 4.118A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.664A pdb=" N TRP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 272 through 320 removed outlier: 4.193A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.622A pdb=" N GLU B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.628A pdb=" N SER B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.680A pdb=" N GLU B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 416 removed outlier: 3.663A pdb=" N TRP B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.525A pdb=" N SER B 426 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 427' Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.629A pdb=" N GLY B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.885A pdb=" N TRP B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 483 removed outlier: 3.828A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 512 through 532 removed outlier: 4.356A pdb=" N ASP B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 3.594A pdb=" N LEU B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.921A pdb=" N LEU B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.597A pdb=" N ASP C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 80 removed outlier: 3.850A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.684A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.992A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 130 removed outlier: 3.566A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.535A pdb=" N MET C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.592A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 Proline residue: C 178 - end of helix removed outlier: 3.751A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.907A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.615A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.528A pdb=" N GLY C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 366 through 383 removed outlier: 4.030A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.699A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 410 removed outlier: 3.606A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.728A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.630A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 449 through 464 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.817A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.648A pdb=" N ASN C 508 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 509 " --> pdb=" O VAL C 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 509' Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.988A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.593A pdb=" N LYS C 541 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 4.312A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.521A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.818A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.612A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.518A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.566A pdb=" N VAL C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 3.513A pdb=" N VAL C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE C 761 " --> pdb=" O ILE C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.971A pdb=" N VAL D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.203A pdb=" N VAL D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.639A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.621A pdb=" N LEU D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.688A pdb=" N LEU D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.635A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 84 Processing helix chain 'D' and resid 85 through 116 removed outlier: 4.202A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.613A pdb=" N LYS D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 192 through 202 removed outlier: 4.118A pdb=" N ALA D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.664A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 272 through 320 removed outlier: 4.192A pdb=" N ILE D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL D 313 " --> pdb=" O CYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 340 removed outlier: 3.622A pdb=" N GLU D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.628A pdb=" N SER D 349 " --> pdb=" O PRO D 345 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.680A pdb=" N GLU D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 416 removed outlier: 3.663A pdb=" N TRP D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.525A pdb=" N SER D 426 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 427' Processing helix chain 'D' and resid 431 through 445 removed outlier: 3.630A pdb=" N GLY D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.885A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 483 removed outlier: 3.828A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 477 " --> pdb=" O VAL D 473 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D 482 " --> pdb=" O ILE D 478 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 491 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.356A pdb=" N ASP D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU D 530 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 532 " --> pdb=" O TYR D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 3.595A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.920A pdb=" N LEU D 572 " --> pdb=" O MET D 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.923A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.726A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 removed outlier: 6.731A pdb=" N ASP A 693 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'B' and resid 535 through 538 Processing sheet with id=AA7, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.924A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.727A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 670 through 673 removed outlier: 6.731A pdb=" N ASP C 693 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AB3, first strand: chain 'D' and resid 535 through 538 1045 hydrogen bonds defined for protein. 3045 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: 7.75 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6807 1.35 - 1.48: 6383 1.48 - 1.62: 8932 1.62 - 1.75: 0 1.75 - 1.88: 216 Bond restraints: 22338 Sorted by residual: bond pdb=" CA THR B 192 " pdb=" C THR B 192 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" CA THR D 192 " pdb=" C THR D 192 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" N PRO C 677 " pdb=" CD PRO C 677 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.86e+01 bond pdb=" N PRO A 677 " pdb=" CD PRO A 677 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N THR B 192 " pdb=" CA THR B 192 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.29e-02 6.01e+03 1.80e+01 ... (remaining 22333 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.78: 689 106.78 - 114.71: 13251 114.71 - 122.64: 14482 122.64 - 130.57: 1820 130.57 - 138.50: 140 Bond angle restraints: 30382 Sorted by residual: angle pdb=" N GLY B 193 " pdb=" CA GLY B 193 " pdb=" C GLY B 193 " ideal model delta sigma weight residual 112.64 118.43 -5.79 1.21e+00 6.83e-01 2.29e+01 angle pdb=" N GLY D 193 " pdb=" CA GLY D 193 " pdb=" C GLY D 193 " ideal model delta sigma weight residual 112.64 118.43 -5.79 1.21e+00 6.83e-01 2.29e+01 angle pdb=" C VAL D 45 " pdb=" N PRO D 46 " pdb=" CA PRO D 46 " ideal model delta sigma weight residual 119.05 113.78 5.27 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C VAL B 45 " pdb=" N PRO B 46 " pdb=" CA PRO B 46 " ideal model delta sigma weight residual 119.05 113.78 5.27 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C PHE D 228 " pdb=" N THR D 229 " pdb=" CA THR D 229 " ideal model delta sigma weight residual 120.49 113.77 6.72 1.42e+00 4.96e-01 2.24e+01 ... (remaining 30377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11637 17.75 - 35.50: 1339 35.50 - 53.25: 408 53.25 - 71.00: 96 71.00 - 88.75: 38 Dihedral angle restraints: 13518 sinusoidal: 5740 harmonic: 7778 Sorted by residual: dihedral pdb=" CA ALA D 500 " pdb=" C ALA D 500 " pdb=" N VAL D 501 " pdb=" CA VAL D 501 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ALA B 500 " pdb=" C ALA B 500 " pdb=" N VAL B 501 " pdb=" CA VAL B 501 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 46.42 46.58 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 13515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 3396 0.186 - 0.373: 24 0.373 - 0.559: 0 0.559 - 0.746: 0 0.746 - 0.932: 2 Chirality restraints: 3422 Sorted by residual: chirality pdb=" C1 NAG D 703 " pdb=" ND2 ASN D 131 " pdb=" C2 NAG D 703 " pdb=" O5 NAG D 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 131 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CA TYR D 463 " pdb=" N TYR D 463 " pdb=" C TYR D 463 " pdb=" CB TYR D 463 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3419 not shown) Planarity restraints: 3808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 131 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.59e+01 pdb=" CG ASN B 131 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 131 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN B 131 " -0.081 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 131 " -0.022 2.00e-02 2.50e+03 4.56e-02 2.59e+01 pdb=" CG ASN D 131 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 131 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN D 131 " 0.081 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 732 " -0.063 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO A 733 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " -0.051 5.00e-02 4.00e+02 ... (remaining 3805 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 144 2.45 - 3.06: 16119 3.06 - 3.67: 30575 3.67 - 4.29: 45658 4.29 - 4.90: 76502 Nonbonded interactions: 168998 Sorted by model distance: nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.837 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.837 2.230 nonbonded pdb=" O TYR B 265 " pdb=" O ASN B 266 " model vdw 1.948 3.040 nonbonded pdb=" O TYR D 265 " pdb=" O ASN D 266 " model vdw 1.948 3.040 nonbonded pdb=" O GLY D 485 " pdb=" N ARG D 487 " model vdw 2.027 2.520 ... (remaining 168993 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' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic 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: 1.850 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: 0.030 Extract box with map and model: 6.370 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 62.420 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5054 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 0.075 22338 Z= 0.697 Angle : 1.027 13.496 30382 Z= 0.601 Chirality : 0.062 0.932 3422 Planarity : 0.005 0.096 3790 Dihedral : 17.225 88.753 8496 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 2.15 % Allowed : 12.88 % Favored : 84.97 % Rotamer: Outliers : 8.31 % Allowed : 15.93 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -4.52 (0.13), residues: 2648 helix: -2.56 (0.10), residues: 1562 sheet: -2.13 (0.57), residues: 68 loop : -3.64 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 509 HIS 0.007 0.002 HIS C 417 PHE 0.014 0.002 PHE A 274 TYR 0.022 0.002 TYR C 183 ARG 0.020 0.001 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 556 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8063 (mp10) cc_final: 0.7744 (pm20) REVERT: A 154 ASN cc_start: 0.7847 (m110) cc_final: 0.7589 (m-40) REVERT: A 190 MET cc_start: 0.7952 (tmt) cc_final: 0.7605 (tmm) REVERT: A 199 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.5261 (t80) REVERT: A 210 ASN cc_start: 0.8639 (m-40) cc_final: 0.8189 (m-40) REVERT: A 276 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 309 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7831 (mmtp) REVERT: A 330 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7829 (p0) REVERT: A 350 ASP cc_start: 0.5858 (t0) cc_final: 0.5542 (t70) REVERT: A 470 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7480 (ttmt) REVERT: A 559 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7445 (ptm-80) REVERT: A 568 LEU cc_start: 0.8230 (tp) cc_final: 0.7968 (tt) REVERT: A 572 ASN cc_start: 0.8587 (m-40) cc_final: 0.8246 (m-40) REVERT: A 577 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: A 601 ASN cc_start: 0.7091 (m-40) cc_final: 0.6883 (p0) REVERT: A 640 MET cc_start: 0.7358 (mmm) cc_final: 0.7113 (mmm) REVERT: A 651 MET cc_start: 0.7745 (mmm) cc_final: 0.7482 (mmm) REVERT: A 662 MET cc_start: 0.6406 (tpt) cc_final: 0.5961 (tpp) REVERT: A 760 LEU cc_start: 0.2040 (OUTLIER) cc_final: 0.1809 (tt) REVERT: B 101 TYR cc_start: 0.7121 (p90) cc_final: 0.6561 (p90) REVERT: B 136 ASP cc_start: 0.6947 (t0) cc_final: 0.6457 (p0) REVERT: B 324 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5550 (pm20) REVERT: B 333 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.2853 (tp) REVERT: B 359 SER cc_start: 0.7524 (t) cc_final: 0.7181 (p) REVERT: B 380 GLU cc_start: 0.4954 (mm-30) cc_final: 0.4054 (mm-30) REVERT: B 406 SER cc_start: 0.6705 (OUTLIER) cc_final: 0.6486 (p) REVERT: B 473 VAL cc_start: 0.7218 (t) cc_final: 0.6929 (t) REVERT: C 113 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6771 (p) REVERT: C 156 LEU cc_start: 0.8465 (mt) cc_final: 0.8191 (tp) REVERT: C 182 GLU cc_start: 0.5355 (tt0) cc_final: 0.5081 (mt-10) REVERT: C 330 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7825 (p0) REVERT: C 366 MET cc_start: 0.8051 (ttt) cc_final: 0.7823 (ttm) REVERT: C 383 MET cc_start: 0.8245 (mtp) cc_final: 0.8022 (mtt) REVERT: C 408 MET cc_start: 0.8599 (mpp) cc_final: 0.8319 (mmm) REVERT: C 416 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8338 (ttpt) REVERT: C 625 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7708 (mttt) REVERT: C 637 ASP cc_start: 0.7164 (m-30) cc_final: 0.6865 (m-30) REVERT: C 667 GLU cc_start: 0.5884 (pp20) cc_final: 0.5174 (mp0) REVERT: C 668 GLU cc_start: 0.7702 (pm20) cc_final: 0.7367 (pm20) REVERT: C 669 ASP cc_start: 0.6895 (m-30) cc_final: 0.6668 (m-30) REVERT: C 740 SER cc_start: 0.1268 (OUTLIER) cc_final: 0.1064 (m) REVERT: D 38 TYR cc_start: 0.3966 (m-80) cc_final: 0.3173 (m-80) REVERT: D 187 ARG cc_start: 0.3551 (OUTLIER) cc_final: 0.3339 (mtt180) REVERT: D 281 LEU cc_start: 0.7763 (mt) cc_final: 0.7522 (tp) REVERT: D 324 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5665 (mm-30) REVERT: D 334 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: D 344 TYR cc_start: 0.7544 (m-80) cc_final: 0.6777 (m-80) outliers start: 192 outliers final: 38 residues processed: 707 average time/residue: 0.3259 time to fit residues: 352.9179 Evaluate side-chains 391 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 339 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 149 ASN A 154 ASN A 250 ASN A 345 HIS A 493 HIS A 505 HIS A 556 ASN A 586 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 736 GLN B 36 GLN B 118 GLN B 243 ASN B 275 HIS B 283 ASN B 410 ASN B 537 GLN C 33 ASN C 42 GLN C 63 ASN C 149 ASN C 154 ASN C 239 HIS C 250 ASN C 345 HIS C 493 HIS C 505 HIS C 556 ASN C 586 ASN C 599 ASN C 682 ASN C 736 GLN D 36 GLN D 67 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 243 ASN D 283 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5209 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22338 Z= 0.248 Angle : 0.749 10.713 30382 Z= 0.377 Chirality : 0.047 0.262 3422 Planarity : 0.005 0.094 3790 Dihedral : 9.027 88.637 3639 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.23 % Favored : 91.54 % Rotamer: Outliers : 4.63 % Allowed : 19.83 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.38 (0.16), residues: 2648 helix: -0.73 (0.13), residues: 1566 sheet: -1.53 (0.56), residues: 82 loop : -2.92 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 509 HIS 0.009 0.001 HIS C 417 PHE 0.028 0.002 PHE A 746 TYR 0.022 0.002 TYR B 210 ARG 0.007 0.001 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 362 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.7904 (m-40) cc_final: 0.7659 (m-40) REVERT: A 190 MET cc_start: 0.7794 (tmt) cc_final: 0.7444 (tmm) REVERT: A 228 HIS cc_start: 0.6477 (t70) cc_final: 0.5355 (m170) REVERT: A 276 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 332 MET cc_start: 0.8637 (tpp) cc_final: 0.8207 (tpp) REVERT: A 376 MET cc_start: 0.7794 (mtp) cc_final: 0.7560 (mtp) REVERT: A 470 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7624 (ttmt) REVERT: A 559 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7413 (ptm-80) REVERT: A 560 LEU cc_start: 0.8008 (mt) cc_final: 0.7768 (mp) REVERT: A 572 ASN cc_start: 0.8352 (m-40) cc_final: 0.8026 (m-40) REVERT: A 662 MET cc_start: 0.6651 (tpt) cc_final: 0.6278 (tpp) REVERT: A 757 ILE cc_start: 0.1899 (OUTLIER) cc_final: 0.1649 (tp) REVERT: A 760 LEU cc_start: 0.1953 (OUTLIER) cc_final: 0.1732 (tp) REVERT: B 101 TYR cc_start: 0.6919 (p90) cc_final: 0.6216 (p90) REVERT: B 136 ASP cc_start: 0.6521 (t0) cc_final: 0.5957 (p0) REVERT: B 324 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: B 524 TYR cc_start: 0.5970 (t80) cc_final: 0.5734 (t80) REVERT: C 83 TYR cc_start: 0.7729 (m-10) cc_final: 0.7471 (m-10) REVERT: C 140 GLU cc_start: 0.6888 (pt0) cc_final: 0.6260 (pt0) REVERT: C 156 LEU cc_start: 0.8539 (mt) cc_final: 0.8269 (tp) REVERT: C 219 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7218 (mtm-85) REVERT: C 228 HIS cc_start: 0.5963 (t70) cc_final: 0.5505 (m170) REVERT: C 313 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8593 (mtmt) REVERT: C 383 MET cc_start: 0.8154 (mtp) cc_final: 0.7886 (mtt) REVERT: C 408 MET cc_start: 0.8577 (tpp) cc_final: 0.8153 (mmm) REVERT: C 433 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: C 446 ILE cc_start: 0.8177 (mm) cc_final: 0.7965 (mt) REVERT: C 474 MET cc_start: 0.6838 (mmp) cc_final: 0.6605 (mmp) REVERT: C 625 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7761 (mttt) REVERT: C 662 MET cc_start: 0.8070 (tpp) cc_final: 0.7532 (tpt) REVERT: C 667 GLU cc_start: 0.6858 (pp20) cc_final: 0.6241 (mp0) REVERT: C 669 ASP cc_start: 0.7577 (m-30) cc_final: 0.7367 (m-30) REVERT: D 38 TYR cc_start: 0.4415 (m-80) cc_final: 0.3563 (m-80) REVERT: D 69 MET cc_start: 0.5912 (mmt) cc_final: 0.5546 (mmt) REVERT: D 139 CYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3314 (t) REVERT: D 149 TRP cc_start: 0.5952 (t60) cc_final: 0.5355 (t-100) REVERT: D 202 LEU cc_start: 0.6148 (tp) cc_final: 0.5902 (tp) REVERT: D 324 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5839 (mt-10) REVERT: D 351 MET cc_start: 0.7098 (ttm) cc_final: 0.6797 (ttm) REVERT: D 398 MET cc_start: 0.7057 (tmm) cc_final: 0.6833 (tmm) REVERT: D 444 ILE cc_start: 0.5831 (mm) cc_final: 0.5610 (mt) outliers start: 107 outliers final: 45 residues processed: 448 average time/residue: 0.2923 time to fit residues: 212.1443 Evaluate side-chains 329 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 277 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN A 340 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5304 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22338 Z= 0.238 Angle : 0.666 10.854 30382 Z= 0.334 Chirality : 0.045 0.309 3422 Planarity : 0.005 0.079 3790 Dihedral : 7.078 62.652 3584 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.82 % Favored : 91.88 % Rotamer: Outliers : 3.68 % Allowed : 20.52 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.51 (0.16), residues: 2648 helix: -0.07 (0.13), residues: 1594 sheet: -1.36 (0.54), residues: 82 loop : -2.53 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 168 HIS 0.007 0.001 HIS A 241 PHE 0.025 0.002 PHE B 110 TYR 0.014 0.001 TYR D 182 ARG 0.011 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 300 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8735 (p) REVERT: A 150 GLU cc_start: 0.6443 (pp20) cc_final: 0.5966 (pt0) REVERT: A 190 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7356 (tmm) REVERT: A 206 ASP cc_start: 0.8241 (t0) cc_final: 0.8016 (t0) REVERT: A 228 HIS cc_start: 0.6564 (t70) cc_final: 0.5564 (m170) REVERT: A 332 MET cc_start: 0.8517 (tpp) cc_final: 0.7928 (tpp) REVERT: A 360 MET cc_start: 0.7264 (ttp) cc_final: 0.6910 (ttp) REVERT: A 479 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6589 (mt-10) REVERT: A 572 ASN cc_start: 0.8624 (m-40) cc_final: 0.8398 (m-40) REVERT: A 660 ASN cc_start: 0.8156 (m-40) cc_final: 0.7792 (m-40) REVERT: B 101 TYR cc_start: 0.7080 (p90) cc_final: 0.6453 (p90) REVERT: B 225 MET cc_start: 0.6998 (tpp) cc_final: 0.6781 (ptm) REVERT: B 324 GLU cc_start: 0.6322 (tp30) cc_final: 0.5633 (mp0) REVERT: B 335 GLN cc_start: 0.5842 (mp10) cc_final: 0.5583 (tp-100) REVERT: B 380 GLU cc_start: 0.5116 (mm-30) cc_final: 0.4351 (tp30) REVERT: C 228 HIS cc_start: 0.6526 (t70) cc_final: 0.5835 (m170) REVERT: C 313 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8680 (mtmt) REVERT: C 323 MET cc_start: 0.7746 (mmt) cc_final: 0.7534 (tpp) REVERT: C 330 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.7759 (p0) REVERT: C 383 MET cc_start: 0.8098 (mtp) cc_final: 0.7800 (mtt) REVERT: C 401 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: C 408 MET cc_start: 0.8701 (tpp) cc_final: 0.8030 (mmm) REVERT: C 416 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8153 (tttp) REVERT: C 433 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: C 471 ASP cc_start: 0.7781 (t0) cc_final: 0.7387 (t0) REVERT: C 480 MET cc_start: 0.7955 (mtp) cc_final: 0.7744 (mtm) REVERT: C 625 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7811 (mttt) REVERT: C 662 MET cc_start: 0.8114 (tpp) cc_final: 0.7646 (tpt) REVERT: D 69 MET cc_start: 0.5800 (mmt) cc_final: 0.5568 (mmt) REVERT: D 139 CYS cc_start: 0.3952 (OUTLIER) cc_final: 0.3458 (t) REVERT: D 324 GLU cc_start: 0.6016 (tp30) cc_final: 0.5809 (mm-30) outliers start: 85 outliers final: 46 residues processed: 365 average time/residue: 0.2953 time to fit residues: 177.1991 Evaluate side-chains 298 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 246 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 570 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.0270 chunk 179 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 253 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN C 64 ASN D 115 HIS D 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22338 Z= 0.221 Angle : 0.634 10.235 30382 Z= 0.316 Chirality : 0.044 0.292 3422 Planarity : 0.004 0.072 3790 Dihedral : 6.204 59.946 3566 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 3.85 % Allowed : 21.52 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.14 (0.16), residues: 2648 helix: 0.21 (0.13), residues: 1618 sheet: -1.23 (0.54), residues: 82 loop : -2.40 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 149 HIS 0.007 0.001 HIS C 417 PHE 0.024 0.002 PHE D 110 TYR 0.033 0.001 TYR C 83 ARG 0.004 0.000 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 256 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 150 GLU cc_start: 0.6301 (pp20) cc_final: 0.5898 (pt0) REVERT: A 190 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7233 (tmm) REVERT: A 206 ASP cc_start: 0.8308 (t0) cc_final: 0.7916 (t0) REVERT: A 228 HIS cc_start: 0.6677 (t70) cc_final: 0.5593 (m170) REVERT: A 323 MET cc_start: 0.6132 (mmm) cc_final: 0.5373 (mmm) REVERT: A 332 MET cc_start: 0.8472 (tpp) cc_final: 0.8105 (tpp) REVERT: A 360 MET cc_start: 0.7108 (ttp) cc_final: 0.6687 (ttp) REVERT: A 479 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6645 (mt-10) REVERT: A 660 ASN cc_start: 0.8408 (m-40) cc_final: 0.8019 (m-40) REVERT: B 101 TYR cc_start: 0.7098 (p90) cc_final: 0.6898 (p90) REVERT: B 324 GLU cc_start: 0.6267 (tp30) cc_final: 0.5563 (mp0) REVERT: B 335 GLN cc_start: 0.5832 (mp10) cc_final: 0.5592 (tp-100) REVERT: C 50 TYR cc_start: 0.7116 (t80) cc_final: 0.6907 (t80) REVERT: C 219 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7828 (mtm180) REVERT: C 228 HIS cc_start: 0.6709 (t70) cc_final: 0.5974 (m170) REVERT: C 313 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8702 (mtmt) REVERT: C 330 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.7731 (p0) REVERT: C 383 MET cc_start: 0.8112 (mtp) cc_final: 0.7851 (mtt) REVERT: C 401 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7674 (t-90) REVERT: C 408 MET cc_start: 0.8700 (tpp) cc_final: 0.8093 (mmm) REVERT: C 416 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8195 (tttp) REVERT: C 433 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: C 467 GLU cc_start: 0.7824 (tt0) cc_final: 0.7546 (mt-10) REVERT: C 556 ASN cc_start: 0.8357 (t0) cc_final: 0.8126 (t0) REVERT: C 625 LYS cc_start: 0.8456 (mtpt) cc_final: 0.7889 (mttt) REVERT: C 662 MET cc_start: 0.8031 (tpp) cc_final: 0.7587 (tpt) REVERT: D 139 CYS cc_start: 0.4130 (OUTLIER) cc_final: 0.3580 (t) REVERT: D 205 CYS cc_start: 0.5463 (OUTLIER) cc_final: 0.4576 (m) REVERT: D 446 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6886 (mmp) outliers start: 89 outliers final: 48 residues processed: 320 average time/residue: 0.2896 time to fit residues: 152.4748 Evaluate side-chains 294 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 238 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 730 THR Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 10.0000 chunk 143 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 216 optimal weight: 0.0030 chunk 175 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5359 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22338 Z= 0.230 Angle : 0.619 9.982 30382 Z= 0.306 Chirality : 0.043 0.306 3422 Planarity : 0.004 0.061 3790 Dihedral : 5.826 59.909 3562 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 3.03 % Allowed : 22.77 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.92 (0.16), residues: 2648 helix: 0.37 (0.13), residues: 1634 sheet: -1.29 (0.53), residues: 82 loop : -2.31 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 149 HIS 0.007 0.001 HIS A 241 PHE 0.029 0.001 PHE D 110 TYR 0.018 0.001 TYR C 83 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 247 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 82 MET cc_start: 0.7957 (mtm) cc_final: 0.7733 (mtt) REVERT: A 150 GLU cc_start: 0.6189 (pp20) cc_final: 0.5790 (pt0) REVERT: A 190 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7209 (tmm) REVERT: A 206 ASP cc_start: 0.8442 (t0) cc_final: 0.8018 (t0) REVERT: A 228 HIS cc_start: 0.6898 (t70) cc_final: 0.5872 (m170) REVERT: A 332 MET cc_start: 0.8356 (tpp) cc_final: 0.7798 (tpp) REVERT: A 360 MET cc_start: 0.7091 (ttp) cc_final: 0.6539 (ttp) REVERT: A 479 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 660 ASN cc_start: 0.8422 (m-40) cc_final: 0.8032 (m-40) REVERT: B 183 LEU cc_start: 0.6140 (tt) cc_final: 0.5846 (tp) REVERT: B 225 MET cc_start: 0.7197 (tpp) cc_final: 0.6801 (ptm) REVERT: B 335 GLN cc_start: 0.5833 (mp10) cc_final: 0.5597 (tp-100) REVERT: C 219 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7933 (mtm180) REVERT: C 228 HIS cc_start: 0.6832 (t70) cc_final: 0.6224 (m170) REVERT: C 313 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8707 (mtmt) REVERT: C 330 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7750 (p0) REVERT: C 383 MET cc_start: 0.8198 (mtp) cc_final: 0.7916 (mtt) REVERT: C 401 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7802 (t-90) REVERT: C 408 MET cc_start: 0.8750 (tpp) cc_final: 0.8182 (mmm) REVERT: C 416 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8278 (tttp) REVERT: C 433 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: C 467 GLU cc_start: 0.7803 (tt0) cc_final: 0.7572 (mt-10) REVERT: C 564 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: C 625 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7791 (mttt) REVERT: C 662 MET cc_start: 0.7931 (tpp) cc_final: 0.7594 (tpt) REVERT: D 139 CYS cc_start: 0.4406 (OUTLIER) cc_final: 0.3870 (t) REVERT: D 183 LEU cc_start: 0.5583 (tt) cc_final: 0.5269 (pp) outliers start: 70 outliers final: 49 residues processed: 301 average time/residue: 0.2819 time to fit residues: 140.4282 Evaluate side-chains 284 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 253 optimal weight: 40.0000 chunk 210 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22338 Z= 0.232 Angle : 0.607 10.007 30382 Z= 0.302 Chirality : 0.043 0.315 3422 Planarity : 0.004 0.053 3790 Dihedral : 5.477 59.901 3557 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.65 % Favored : 93.09 % Rotamer: Outliers : 3.16 % Allowed : 22.90 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.79 (0.17), residues: 2648 helix: 0.52 (0.13), residues: 1640 sheet: -1.35 (0.52), residues: 82 loop : -2.36 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 149 HIS 0.007 0.001 HIS A 241 PHE 0.026 0.002 PHE D 114 TYR 0.025 0.001 TYR A 50 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 244 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8001 (mtm) cc_final: 0.7696 (mtt) REVERT: A 150 GLU cc_start: 0.6145 (pp20) cc_final: 0.5749 (pt0) REVERT: A 190 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7199 (tmm) REVERT: A 206 ASP cc_start: 0.8549 (t0) cc_final: 0.8076 (t0) REVERT: A 228 HIS cc_start: 0.6958 (t70) cc_final: 0.5891 (m170) REVERT: A 323 MET cc_start: 0.6012 (mmm) cc_final: 0.5403 (mmm) REVERT: A 332 MET cc_start: 0.8323 (tpp) cc_final: 0.8100 (tpp) REVERT: A 411 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 416 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8187 (tptp) REVERT: A 479 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 660 ASN cc_start: 0.8454 (m-40) cc_final: 0.8041 (m-40) REVERT: B 335 GLN cc_start: 0.5972 (mp10) cc_final: 0.5734 (tp-100) REVERT: C 228 HIS cc_start: 0.6890 (t70) cc_final: 0.6155 (m90) REVERT: C 313 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8772 (mtmt) REVERT: C 330 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7703 (p0) REVERT: C 376 MET cc_start: 0.8386 (tpp) cc_final: 0.7473 (ttt) REVERT: C 383 MET cc_start: 0.8225 (mtp) cc_final: 0.8003 (mtt) REVERT: C 401 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.7979 (t-90) REVERT: C 408 MET cc_start: 0.8601 (tpp) cc_final: 0.8257 (mmm) REVERT: C 416 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8380 (tttp) REVERT: C 433 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: C 467 GLU cc_start: 0.7776 (tt0) cc_final: 0.7549 (mt-10) REVERT: C 564 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: C 625 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7861 (mttt) REVERT: C 662 MET cc_start: 0.7932 (tpp) cc_final: 0.7605 (tpt) REVERT: C 668 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: D 69 MET cc_start: 0.5501 (mmt) cc_final: 0.5003 (mmt) REVERT: D 139 CYS cc_start: 0.4330 (OUTLIER) cc_final: 0.3897 (t) outliers start: 73 outliers final: 52 residues processed: 300 average time/residue: 0.2878 time to fit residues: 141.9556 Evaluate side-chains 288 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 228 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 252 optimal weight: 0.0870 chunk 158 optimal weight: 0.0570 chunk 153 optimal weight: 1.9990 chunk 116 optimal weight: 0.0770 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 599 ASN C 24 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22338 Z= 0.142 Angle : 0.571 10.338 30382 Z= 0.281 Chirality : 0.041 0.314 3422 Planarity : 0.004 0.053 3790 Dihedral : 5.209 59.880 3556 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.23 % Favored : 93.54 % Rotamer: Outliers : 2.38 % Allowed : 24.24 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.49 (0.17), residues: 2648 helix: 0.76 (0.13), residues: 1628 sheet: -1.40 (0.52), residues: 82 loop : -2.19 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 149 HIS 0.005 0.001 HIS C 417 PHE 0.018 0.001 PHE D 228 TYR 0.021 0.001 TYR D 182 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 242 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8028 (mtm) cc_final: 0.7740 (mtt) REVERT: A 150 GLU cc_start: 0.6081 (pp20) cc_final: 0.5696 (pt0) REVERT: A 190 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7199 (tmm) REVERT: A 206 ASP cc_start: 0.8485 (t0) cc_final: 0.7983 (t0) REVERT: A 228 HIS cc_start: 0.6995 (t70) cc_final: 0.5825 (m170) REVERT: A 332 MET cc_start: 0.8282 (tpp) cc_final: 0.8036 (tpp) REVERT: A 416 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8133 (tptp) REVERT: A 479 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6763 (mt-10) REVERT: B 225 MET cc_start: 0.7129 (tpp) cc_final: 0.6686 (ptm) REVERT: B 335 GLN cc_start: 0.5931 (mp10) cc_final: 0.5692 (tp-100) REVERT: C 228 HIS cc_start: 0.6934 (t70) cc_final: 0.6114 (m170) REVERT: C 313 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8718 (mtmt) REVERT: C 330 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7701 (p0) REVERT: C 401 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.7936 (t-90) REVERT: C 408 MET cc_start: 0.8591 (tpp) cc_final: 0.7802 (mmm) REVERT: C 416 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8246 (tttp) REVERT: C 433 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: C 467 GLU cc_start: 0.7690 (tt0) cc_final: 0.7479 (mt-10) REVERT: C 564 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: C 625 LYS cc_start: 0.8388 (mtpt) cc_final: 0.7965 (mttt) REVERT: C 662 MET cc_start: 0.7908 (tpp) cc_final: 0.7613 (tpt) REVERT: D 69 MET cc_start: 0.5414 (mmt) cc_final: 0.4878 (mmt) REVERT: D 139 CYS cc_start: 0.4207 (OUTLIER) cc_final: 0.3802 (t) outliers start: 55 outliers final: 36 residues processed: 280 average time/residue: 0.3062 time to fit residues: 139.3856 Evaluate side-chains 271 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 150 optimal weight: 0.0010 chunk 76 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5334 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22338 Z= 0.152 Angle : 0.563 10.660 30382 Z= 0.276 Chirality : 0.041 0.327 3422 Planarity : 0.004 0.047 3790 Dihedral : 5.029 58.860 3556 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.19 % Favored : 93.62 % Rotamer: Outliers : 2.12 % Allowed : 24.42 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2648 helix: 0.84 (0.13), residues: 1632 sheet: -1.37 (0.52), residues: 82 loop : -2.14 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 149 HIS 0.005 0.001 HIS C 417 PHE 0.019 0.001 PHE D 228 TYR 0.026 0.001 TYR D 182 ARG 0.007 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 241 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7997 (mtm) cc_final: 0.7717 (mtt) REVERT: A 150 GLU cc_start: 0.6120 (pp20) cc_final: 0.5733 (pt0) REVERT: A 190 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7185 (tmm) REVERT: A 206 ASP cc_start: 0.8436 (t0) cc_final: 0.7934 (t0) REVERT: A 228 HIS cc_start: 0.7008 (t70) cc_final: 0.5866 (m170) REVERT: A 332 MET cc_start: 0.8266 (tpp) cc_final: 0.8041 (tpp) REVERT: A 416 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8140 (tptp) REVERT: A 479 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6754 (mt-10) REVERT: B 225 MET cc_start: 0.7036 (tpp) cc_final: 0.6705 (ptm) REVERT: B 335 GLN cc_start: 0.5900 (mp10) cc_final: 0.5639 (tp-100) REVERT: C 228 HIS cc_start: 0.6997 (t70) cc_final: 0.6131 (m170) REVERT: C 231 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7430 (mm-30) REVERT: C 313 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8719 (mtmt) REVERT: C 330 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7653 (p0) REVERT: C 401 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8018 (t-90) REVERT: C 408 MET cc_start: 0.8579 (tpp) cc_final: 0.7785 (mmm) REVERT: C 416 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8270 (tttp) REVERT: C 433 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6768 (tt0) REVERT: C 467 GLU cc_start: 0.7669 (tt0) cc_final: 0.7437 (mt-10) REVERT: C 564 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: C 625 LYS cc_start: 0.8471 (mtpt) cc_final: 0.7980 (mttt) REVERT: C 662 MET cc_start: 0.7909 (tpp) cc_final: 0.7628 (tpt) REVERT: D 69 MET cc_start: 0.5396 (mmt) cc_final: 0.4907 (mmt) REVERT: D 139 CYS cc_start: 0.4317 (OUTLIER) cc_final: 0.3922 (t) outliers start: 49 outliers final: 37 residues processed: 274 average time/residue: 0.3003 time to fit residues: 134.0560 Evaluate side-chains 272 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 chunk 234 optimal weight: 0.0770 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 22338 Z= 0.339 Angle : 0.646 10.748 30382 Z= 0.321 Chirality : 0.045 0.336 3422 Planarity : 0.004 0.045 3790 Dihedral : 5.156 58.838 3555 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 2.47 % Allowed : 24.72 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.62 (0.17), residues: 2648 helix: 0.63 (0.13), residues: 1632 sheet: -1.38 (0.52), residues: 82 loop : -2.22 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 149 HIS 0.010 0.001 HIS A 241 PHE 0.035 0.002 PHE D 117 TYR 0.023 0.002 TYR C 50 ARG 0.004 0.000 ARG C 652 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 231 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8060 (mtm) cc_final: 0.7793 (mtt) REVERT: A 150 GLU cc_start: 0.6098 (pp20) cc_final: 0.5771 (pt0) REVERT: A 152 MET cc_start: 0.7253 (mmt) cc_final: 0.5549 (mmt) REVERT: A 190 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7307 (tmm) REVERT: A 206 ASP cc_start: 0.8595 (t0) cc_final: 0.8133 (t0) REVERT: A 228 HIS cc_start: 0.7048 (t70) cc_final: 0.5975 (m170) REVERT: A 323 MET cc_start: 0.5789 (mmm) cc_final: 0.5538 (mmm) REVERT: A 332 MET cc_start: 0.8251 (tpp) cc_final: 0.8021 (tpp) REVERT: A 416 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8307 (tptp) REVERT: A 479 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 722 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7708 (tp) REVERT: C 150 GLU cc_start: 0.6454 (pp20) cc_final: 0.6235 (tt0) REVERT: C 228 HIS cc_start: 0.7046 (t70) cc_final: 0.6107 (m90) REVERT: C 231 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7462 (mm-30) REVERT: C 313 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8704 (mtmt) REVERT: C 323 MET cc_start: 0.6808 (ttm) cc_final: 0.6436 (ttm) REVERT: C 330 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7577 (p0) REVERT: C 376 MET cc_start: 0.8504 (mmm) cc_final: 0.8149 (tpt) REVERT: C 416 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8409 (tttp) REVERT: C 433 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: C 467 GLU cc_start: 0.7725 (tt0) cc_final: 0.7420 (mt-10) REVERT: C 564 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: C 625 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7890 (mttt) REVERT: C 662 MET cc_start: 0.7857 (tpp) cc_final: 0.7417 (tpt) REVERT: C 668 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: D 38 TYR cc_start: 0.4767 (m-80) cc_final: 0.4003 (m-80) REVERT: D 69 MET cc_start: 0.5447 (mmt) cc_final: 0.4948 (mmt) REVERT: D 139 CYS cc_start: 0.4614 (OUTLIER) cc_final: 0.4096 (t) outliers start: 57 outliers final: 40 residues processed: 275 average time/residue: 0.2868 time to fit residues: 129.5929 Evaluate side-chains 267 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 172 optimal weight: 0.4980 chunk 261 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 218 HIS D 234 GLN D 270 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5365 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22338 Z= 0.184 Angle : 0.586 10.783 30382 Z= 0.288 Chirality : 0.041 0.338 3422 Planarity : 0.004 0.046 3790 Dihedral : 4.947 58.687 3555 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.81 % Rotamer: Outliers : 1.95 % Allowed : 25.28 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2648 helix: 0.79 (0.13), residues: 1638 sheet: -1.31 (0.52), residues: 82 loop : -2.10 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 149 HIS 0.010 0.001 HIS D 218 PHE 0.027 0.001 PHE D 117 TYR 0.024 0.001 TYR C 50 ARG 0.006 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8046 (mtm) cc_final: 0.7787 (mtt) REVERT: A 150 GLU cc_start: 0.5899 (pp20) cc_final: 0.5576 (pt0) REVERT: A 152 MET cc_start: 0.7022 (mmt) cc_final: 0.5530 (mmt) REVERT: A 190 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7249 (tmm) REVERT: A 206 ASP cc_start: 0.8575 (t0) cc_final: 0.8064 (t0) REVERT: A 228 HIS cc_start: 0.7037 (t70) cc_final: 0.5837 (m170) REVERT: A 332 MET cc_start: 0.8206 (tpp) cc_final: 0.7976 (tpp) REVERT: A 416 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8281 (tptp) REVERT: A 479 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6807 (mt-10) REVERT: B 225 MET cc_start: 0.7029 (tpp) cc_final: 0.6719 (ptm) REVERT: C 228 HIS cc_start: 0.7042 (t70) cc_final: 0.6096 (m90) REVERT: C 231 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7435 (mm-30) REVERT: C 323 MET cc_start: 0.6809 (ttm) cc_final: 0.6599 (ttm) REVERT: C 330 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7549 (p0) REVERT: C 401 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8202 (t-90) REVERT: C 416 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8427 (tttp) REVERT: C 433 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: C 467 GLU cc_start: 0.7727 (tt0) cc_final: 0.7170 (mt-10) REVERT: C 564 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: C 625 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7896 (mttt) REVERT: C 662 MET cc_start: 0.7938 (tpp) cc_final: 0.7512 (tpt) REVERT: C 668 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: D 69 MET cc_start: 0.5608 (mmt) cc_final: 0.5259 (mmt) REVERT: D 139 CYS cc_start: 0.4607 (OUTLIER) cc_final: 0.4097 (t) REVERT: D 149 TRP cc_start: 0.6301 (t60) cc_final: 0.5907 (t-100) outliers start: 45 outliers final: 32 residues processed: 270 average time/residue: 0.2965 time to fit residues: 130.6434 Evaluate side-chains 264 residues out of total 2310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 213 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 218 HIS ** D 283 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 = 0.4550 r_free = 0.4550 target = 0.234685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.190248 restraints weight = 25704.575| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.45 r_work: 0.3747 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22338 Z= 0.181 Angle : 0.598 12.384 30382 Z= 0.291 Chirality : 0.042 0.337 3422 Planarity : 0.004 0.048 3790 Dihedral : 4.828 58.644 3555 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.31 % Favored : 93.58 % Rotamer: Outliers : 1.86 % Allowed : 25.37 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.32 (0.17), residues: 2648 helix: 0.83 (0.13), residues: 1646 sheet: -1.25 (0.52), residues: 82 loop : -2.04 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 149 HIS 0.013 0.001 HIS D 218 PHE 0.028 0.001 PHE D 117 TYR 0.025 0.001 TYR C 50 ARG 0.005 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4619.39 seconds wall clock time: 84 minutes 44.25 seconds (5084.25 seconds total)