Starting phenix.real_space_refine on Sun Feb 18 14:55:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/02_2024/8i93_35256.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/02_2024/8i93_35256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/02_2024/8i93_35256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/02_2024/8i93_35256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/02_2024/8i93_35256.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/02_2024/8i93_35256.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 130 5.16 5 C 14476 2.51 5 N 3566 2.21 5 O 4168 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 37": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" 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 ARG 192": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" 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 ARG 192": "NH1" <-> "NH2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ARG 518": "NH1" <-> "NH2" Residue "C GLU 571": "OE1" <-> "OE2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "C PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D GLU 553": "OE1" <-> "OE2" Residue "D GLU 568": "OE1" <-> "OE2" Residue "D ARG 607": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22342 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: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} 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: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.90, per 1000 atoms: 0.58 Number of scatterers: 22342 At special positions: 0 Unit cell: (111.961, 135.875, 182.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 130 16.00 O 4168 8.00 N 3566 7.00 C 14476 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=2.03 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 153 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 383 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 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 153 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 383 " distance=2.03 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 702 " - " ASN B 182 " " NAG B 703 " - " ASN B 158 " " NAG B 704 " - " ASN B 368 " " NAG B 705 " - " ASN B 354 " " NAG C 901 " - " ASN C 322 " " NAG D 702 " - " ASN D 182 " " NAG D 703 " - " ASN D 158 " " NAG D 704 " - " ASN D 368 " " NAG D 705 " - " ASN D 354 " " 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 258 " " 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 258 " Time building additional restraints: 9.65 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5088 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 10 sheets defined 63.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 21 through 52 removed outlier: 3.914A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.170A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 4.115A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.680A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.670A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.558A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.690A 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: 3.883A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.745A 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 293 through 300 Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.508A pdb=" N LYS A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.605A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.815A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.871A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 412 removed outlier: 3.793A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.095A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.751A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.990A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.449A 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: 3.531A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.801A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.749A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.955A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 767 removed outlier: 3.758A pdb=" N GLY A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 765 " --> pdb=" O ILE A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 26 through 30 removed outlier: 4.111A pdb=" N SER B 30 " --> pdb=" O GLU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.774A pdb=" N TYR B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS B 49 " --> pdb=" O CYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 71 through 96 removed outlier: 5.134A pdb=" N ILE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.686A pdb=" N LYS B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 129 removed outlier: 3.995A pdb=" N MET B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 148 through 152 removed outlier: 4.086A pdb=" N ASP B 152 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.580A pdb=" N TRP B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.564A pdb=" N LEU B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 227 removed outlier: 4.436A pdb=" N ALA B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 4.548A pdb=" N THR B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.758A pdb=" N TRP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.871A pdb=" N ASP B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 349 removed outlier: 3.715A pdb=" N ALA B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 320 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.272A pdb=" N ASN B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 355 " --> pdb=" O GLU B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 355' Processing helix chain 'B' and resid 359 through 369 removed outlier: 3.531A pdb=" N ASN B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.697A pdb=" N ALA B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 445 removed outlier: 3.534A pdb=" N TRP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER B 430 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 454 through 470 removed outlier: 4.198A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 508 Proline residue: B 493 - end of helix removed outlier: 3.774A pdb=" N ILE B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 removed outlier: 3.775A pdb=" N PHE B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.525A pdb=" N GLN B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 581 through 591 removed outlier: 4.229A pdb=" N VAL B 585 " --> pdb=" O TRP B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 608 removed outlier: 6.232A pdb=" N ILE B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.584A pdb=" N ASN B 608 " --> pdb=" O LYS B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 52 removed outlier: 3.913A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 4.171A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 4.115A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.679A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.670A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 193 removed outlier: 3.558A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.884A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.745A 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 293 through 300 Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.508A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 removed outlier: 3.605A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 383 removed outlier: 3.814A pdb=" N THR C 371 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.870A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 412 removed outlier: 3.793A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.095A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 Processing helix chain 'C' and resid 449 through 464 Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.752A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 526 " --> pdb=" O GLN C 522 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.991A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.448A 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: 3.530A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.801A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.749A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.955A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 767 removed outlier: 3.758A pdb=" N GLY C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 765 " --> pdb=" O ILE C 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 26 through 30 removed outlier: 4.112A pdb=" N SER D 30 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.775A pdb=" N TYR D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS D 49 " --> pdb=" O CYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 71 through 96 removed outlier: 5.134A pdb=" N ILE D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.685A pdb=" N LYS D 112 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.995A pdb=" N MET D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 148 through 152 removed outlier: 4.086A pdb=" N ASP D 152 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.580A pdb=" N TRP D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.564A pdb=" N LEU D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS D 200 " --> pdb=" O TRP D 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 209 " --> pdb=" O TRP D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 4.436A pdb=" N ALA D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 4.549A pdb=" N THR D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.758A pdb=" N TRP D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 298 through 314 removed outlier: 3.871A pdb=" N ASP D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 349 removed outlier: 3.716A pdb=" N ALA D 318 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D 320 " --> pdb=" O TYR D 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.273A pdb=" N ASN D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL D 355 " --> pdb=" O GLU D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 355' Processing helix chain 'D' and resid 359 through 369 removed outlier: 3.531A pdb=" N ASN D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.696A pdb=" N ALA D 376 " --> pdb=" O PRO D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 445 removed outlier: 3.534A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 418 " --> pdb=" O PRO D 414 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER D 430 " --> pdb=" O CYS D 426 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET D 432 " --> pdb=" O GLY D 428 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 454 through 470 removed outlier: 4.197A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 508 Proline residue: D 493 - end of helix removed outlier: 3.774A pdb=" N ILE D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 506 " --> pdb=" O MET D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 removed outlier: 3.775A pdb=" N PHE D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.526A pdb=" N GLN D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 581 through 591 removed outlier: 4.230A pdb=" N VAL D 585 " --> pdb=" O TRP D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 608 removed outlier: 6.232A pdb=" N ILE D 597 " --> pdb=" O PRO D 593 " (cutoff:3.500A) Proline residue: D 598 - end of helix removed outlier: 3.584A pdb=" N ASN D 608 " --> pdb=" O LYS D 604 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.884A 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: 6.380A 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 Processing sheet with id=AA5, first strand: chain 'B' and resid 559 through 562 removed outlier: 4.148A pdb=" N GLN B 574 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.884A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.380A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AB1, first strand: chain 'D' and resid 559 through 562 removed outlier: 4.148A pdb=" N GLN D 574 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3090 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: 7.03 Time building geometry restraints manager: 10.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6727 1.33 - 1.46: 6245 1.46 - 1.59: 9760 1.59 - 1.72: 0 1.72 - 1.84: 214 Bond restraints: 22946 Sorted by residual: bond pdb=" C ASN A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.337 1.292 0.045 9.80e-03 1.04e+04 2.08e+01 bond pdb=" C ASN C 137 " pdb=" N PRO C 138 " ideal model delta sigma weight residual 1.337 1.293 0.044 9.80e-03 1.04e+04 2.01e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" CB TRP A 461 " pdb=" CG TRP A 461 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.11e+00 bond pdb=" CB TRP C 461 " pdb=" CG TRP C 461 " ideal model delta sigma weight residual 1.498 1.422 0.076 3.10e-02 1.04e+03 6.08e+00 ... (remaining 22941 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.84: 447 104.84 - 112.19: 11509 112.19 - 119.54: 8328 119.54 - 126.89: 10569 126.89 - 134.23: 379 Bond angle restraints: 31232 Sorted by residual: angle pdb=" N GLU B 352 " pdb=" CA GLU B 352 " pdb=" C GLU B 352 " ideal model delta sigma weight residual 111.14 118.60 -7.46 1.08e+00 8.57e-01 4.78e+01 angle pdb=" N GLU D 352 " pdb=" CA GLU D 352 " pdb=" C GLU D 352 " ideal model delta sigma weight residual 111.14 118.58 -7.44 1.08e+00 8.57e-01 4.75e+01 angle pdb=" N ILE D 309 " pdb=" CA ILE D 309 " pdb=" C ILE D 309 " ideal model delta sigma weight residual 113.42 107.21 6.21 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE B 309 " pdb=" CA ILE B 309 " pdb=" C ILE B 309 " ideal model delta sigma weight residual 113.42 107.28 6.14 1.17e+00 7.31e-01 2.76e+01 angle pdb=" N LEU C 656 " pdb=" CA LEU C 656 " pdb=" C LEU C 656 " ideal model delta sigma weight residual 114.62 108.94 5.68 1.14e+00 7.69e-01 2.48e+01 ... (remaining 31227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 12045 17.34 - 34.68: 1348 34.68 - 52.02: 431 52.02 - 69.36: 78 69.36 - 86.70: 46 Dihedral angle restraints: 13948 sinusoidal: 6038 harmonic: 7910 Sorted by residual: dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA CYS C 344 " pdb=" C CYS C 344 " pdb=" N HIS C 345 " pdb=" CA HIS C 345 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA TYR D 174 " pdb=" C TYR D 174 " pdb=" N PHE D 175 " pdb=" CA PHE D 175 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 13945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2274 0.055 - 0.110: 1062 0.110 - 0.164: 157 0.164 - 0.219: 27 0.219 - 0.274: 8 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CB VAL A 463 " pdb=" CA VAL A 463 " pdb=" CG1 VAL A 463 " pdb=" CG2 VAL A 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL C 463 " pdb=" CA VAL C 463 " pdb=" CG1 VAL C 463 " pdb=" CG2 VAL C 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLU D 352 " pdb=" N GLU D 352 " pdb=" C GLU D 352 " pdb=" CB GLU D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3525 not shown) Planarity restraints: 3936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 258 " 0.051 2.00e-02 2.50e+03 5.37e-02 3.60e+01 pdb=" CG ASN D 258 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN D 258 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN D 258 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 258 " 0.051 2.00e-02 2.50e+03 5.36e-02 3.59e+01 pdb=" CG ASN B 258 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B 258 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 258 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 676 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 677 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 677 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 677 " -0.033 5.00e-02 4.00e+02 ... (remaining 3933 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 166 2.51 - 3.11: 17823 3.11 - 3.71: 32692 3.71 - 4.30: 47201 4.30 - 4.90: 78498 Nonbonded interactions: 176380 Sorted by model distance: nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.913 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.913 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 902 " model vdw 2.021 2.230 nonbonded pdb=" OE1 GLU C 402 " pdb="ZN ZN C 902 " model vdw 2.021 2.230 nonbonded pdb=" CE1 HIS C 374 " pdb="ZN ZN C 902 " model vdw 2.109 2.450 ... (remaining 176375 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: 1.240 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: 6.420 Check model and map are aligned: 0.330 Set scattering table: 0.250 Process input model: 61.830 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.014 0.097 22946 Z= 0.933 Angle : 0.970 12.053 31232 Z= 0.544 Chirality : 0.060 0.274 3528 Planarity : 0.005 0.062 3912 Dihedral : 16.714 86.699 8830 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.56 % Favored : 89.37 % Rotamer: Outliers : 3.93 % Allowed : 13.31 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.13), residues: 2700 helix: -1.91 (0.11), residues: 1568 sheet: -1.21 (0.72), residues: 42 loop : -3.47 (0.15), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 566 HIS 0.007 0.002 HIS C 241 PHE 0.035 0.002 PHE B 48 TYR 0.027 0.002 TYR C 385 ARG 0.005 0.001 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 343 time to evaluate : 2.984 Fit side-chains outliers start: 94 outliers final: 36 residues processed: 423 average time/residue: 0.2944 time to fit residues: 203.3968 Evaluate side-chains 188 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain D residue 701 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 112 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 210 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 ASN A 117 ASN A 139 GLN A 149 ASN A 159 ASN A 175 GLN A 239 HIS A 305 GLN A 345 HIS A 374 HIS A 378 HIS A 401 HIS A 437 ASN A 493 HIS A 505 HIS A 522 GLN A 586 ASN A 601 ASN B 8 ASN B 63 GLN B 142 ASN B 340 ASN B 365 GLN B 435 ASN C 58 ASN C 63 ASN C 117 ASN C 139 GLN C 149 ASN C 159 ASN C 175 GLN C 239 HIS C 305 GLN C 345 HIS C 374 HIS C 378 HIS C 401 HIS C 437 ASN C 493 HIS C 505 HIS C 522 GLN C 572 ASN C 586 ASN C 601 ASN D 8 ASN D 63 GLN D 130 ASN D 142 ASN D 340 ASN D 365 GLN D 435 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22946 Z= 0.194 Angle : 0.645 8.414 31232 Z= 0.332 Chirality : 0.043 0.199 3528 Planarity : 0.004 0.041 3912 Dihedral : 8.006 59.342 3773 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 3.05 % Allowed : 16.07 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.15), residues: 2700 helix: -0.65 (0.13), residues: 1602 sheet: -1.08 (0.72), residues: 42 loop : -2.81 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 163 HIS 0.005 0.001 HIS C 378 PHE 0.022 0.002 PHE D 529 TYR 0.022 0.002 TYR C 83 ARG 0.004 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 198 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7410 (ptm) REVERT: A 661 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: A 757 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6560 (mt) REVERT: C 62 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7492 (ptm) REVERT: C 661 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: C 757 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6535 (mt) outliers start: 73 outliers final: 38 residues processed: 254 average time/residue: 0.2886 time to fit residues: 122.5256 Evaluate side-chains 213 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 661 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain D residue 701 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 0.0270 chunk 202 optimal weight: 3.9990 chunk 165 optimal weight: 0.0050 chunk 67 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 overall best weight: 2.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN B 130 ASN B 527 ASN C 139 GLN D 527 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22946 Z= 0.309 Angle : 0.637 8.077 31232 Z= 0.324 Chirality : 0.045 0.193 3528 Planarity : 0.004 0.036 3912 Dihedral : 6.929 57.660 3743 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 3.43 % Allowed : 17.87 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2700 helix: -0.19 (0.13), residues: 1612 sheet: -1.02 (0.74), residues: 42 loop : -2.60 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.011 0.001 HIS A 378 PHE 0.020 0.002 PHE B 48 TYR 0.014 0.002 TYR D 209 ARG 0.004 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 174 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 661 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: C 661 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7972 (mp10) outliers start: 82 outliers final: 41 residues processed: 242 average time/residue: 0.2901 time to fit residues: 118.0636 Evaluate side-chains 198 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 155 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 661 GLN Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN D 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22946 Z= 0.169 Angle : 0.569 10.035 31232 Z= 0.287 Chirality : 0.041 0.261 3528 Planarity : 0.004 0.039 3912 Dihedral : 6.333 58.193 3735 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 2.64 % Allowed : 19.25 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2700 helix: 0.20 (0.13), residues: 1606 sheet: -1.24 (0.73), residues: 42 loop : -2.30 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 PHE 0.019 0.001 PHE B 283 TYR 0.019 0.001 TYR D 209 ARG 0.006 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 701 MET cc_start: 0.6748 (mpp) cc_final: 0.6063 (mpp) REVERT: D 701 MET cc_start: 0.6824 (mpp) cc_final: 0.6107 (mpp) outliers start: 63 outliers final: 40 residues processed: 223 average time/residue: 0.2943 time to fit residues: 110.8809 Evaluate side-chains 189 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 232 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22946 Z= 0.209 Angle : 0.574 10.521 31232 Z= 0.287 Chirality : 0.042 0.184 3528 Planarity : 0.004 0.040 3912 Dihedral : 5.784 59.662 3725 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.56 % Favored : 93.37 % Rotamer: Outliers : 2.59 % Allowed : 19.58 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2700 helix: 0.39 (0.13), residues: 1612 sheet: -1.29 (0.75), residues: 42 loop : -2.18 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.001 PHE B 283 TYR 0.014 0.001 TYR B 209 ARG 0.007 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 160 time to evaluate : 2.730 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.9179 (OUTLIER) cc_final: 0.8470 (t-90) REVERT: C 401 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8483 (t-90) outliers start: 62 outliers final: 44 residues processed: 213 average time/residue: 0.2925 time to fit residues: 107.3398 Evaluate side-chains 193 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22946 Z= 0.165 Angle : 0.546 8.853 31232 Z= 0.273 Chirality : 0.041 0.265 3528 Planarity : 0.004 0.040 3912 Dihedral : 5.328 59.940 3723 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 2.72 % Allowed : 19.50 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2700 helix: 0.64 (0.13), residues: 1608 sheet: -1.34 (0.76), residues: 42 loop : -2.03 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 481 HIS 0.004 0.001 HIS C 241 PHE 0.011 0.001 PHE B 550 TYR 0.014 0.001 TYR D 209 ARG 0.005 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 158 time to evaluate : 2.801 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7125 (ttt90) REVERT: A 401 HIS cc_start: 0.9171 (OUTLIER) cc_final: 0.8550 (t-90) REVERT: C 115 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7123 (ttt90) REVERT: C 401 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8553 (t-90) REVERT: D 85 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6869 (mm) outliers start: 65 outliers final: 37 residues processed: 216 average time/residue: 0.3037 time to fit residues: 110.3314 Evaluate side-chains 187 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 258 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22946 Z= 0.157 Angle : 0.546 9.929 31232 Z= 0.271 Chirality : 0.040 0.209 3528 Planarity : 0.004 0.039 3912 Dihedral : 4.960 59.159 3721 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.26 % Allowed : 20.00 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2700 helix: 0.79 (0.13), residues: 1612 sheet: -1.62 (0.73), residues: 42 loop : -1.97 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 205 HIS 0.003 0.001 HIS C 241 PHE 0.014 0.001 PHE D 546 TYR 0.013 0.001 TYR D 209 ARG 0.005 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 2.895 Fit side-chains REVERT: A 115 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7100 (ttt90) REVERT: A 401 HIS cc_start: 0.9163 (OUTLIER) cc_final: 0.8451 (t-90) REVERT: C 115 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7106 (ttt90) REVERT: C 401 HIS cc_start: 0.9172 (OUTLIER) cc_final: 0.8472 (t-90) outliers start: 54 outliers final: 41 residues processed: 202 average time/residue: 0.2968 time to fit residues: 100.7046 Evaluate side-chains 185 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 140 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 154 optimal weight: 0.0370 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22946 Z= 0.168 Angle : 0.553 9.880 31232 Z= 0.273 Chirality : 0.041 0.273 3528 Planarity : 0.004 0.040 3912 Dihedral : 4.743 59.809 3721 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.34 % Allowed : 20.04 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2700 helix: 0.91 (0.13), residues: 1630 sheet: -1.43 (0.76), residues: 42 loop : -1.94 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS C 241 PHE 0.014 0.001 PHE B 550 TYR 0.011 0.001 TYR D 209 ARG 0.004 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 148 time to evaluate : 2.596 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7081 (ttt90) REVERT: A 401 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8448 (t-90) REVERT: C 115 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7081 (ttt90) REVERT: C 401 HIS cc_start: 0.9174 (OUTLIER) cc_final: 0.8458 (t-90) REVERT: D 85 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.6811 (mm) REVERT: D 701 MET cc_start: 0.6254 (mpp) cc_final: 0.5808 (mpp) outliers start: 56 outliers final: 41 residues processed: 201 average time/residue: 0.2879 time to fit residues: 97.3451 Evaluate side-chains 188 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER 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 723 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.4980 chunk 225 optimal weight: 0.0070 chunk 240 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22946 Z= 0.150 Angle : 0.560 11.160 31232 Z= 0.273 Chirality : 0.040 0.269 3528 Planarity : 0.003 0.039 3912 Dihedral : 4.531 59.011 3721 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.18 % Allowed : 20.21 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2700 helix: 1.02 (0.13), residues: 1630 sheet: -1.69 (0.73), residues: 42 loop : -1.89 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 PHE 0.013 0.001 PHE B 546 TYR 0.023 0.001 TYR B 209 ARG 0.004 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 151 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 ILE cc_start: 0.7167 (mt) cc_final: 0.6950 (tt) REVERT: D 85 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6517 (mm) REVERT: D 225 ILE cc_start: 0.7165 (mt) cc_final: 0.6948 (tt) REVERT: B 701 MET cc_start: 0.6251 (mpp) cc_final: 0.5817 (mpp) REVERT: D 701 MET cc_start: 0.6123 (mpp) cc_final: 0.5750 (mpp) outliers start: 52 outliers final: 36 residues processed: 200 average time/residue: 0.2959 time to fit residues: 100.1620 Evaluate side-chains 179 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 579 MET 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 D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 168 optimal weight: 0.0970 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS B 310 ASN C 401 HIS D 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22946 Z= 0.253 Angle : 0.610 11.950 31232 Z= 0.299 Chirality : 0.043 0.261 3528 Planarity : 0.004 0.041 3912 Dihedral : 4.636 59.658 3719 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.76 % Allowed : 20.25 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2700 helix: 1.00 (0.13), residues: 1626 sheet: -1.20 (0.81), residues: 42 loop : -1.95 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 205 HIS 0.004 0.001 HIS C 378 PHE 0.012 0.001 PHE A 464 TYR 0.023 0.001 TYR D 209 ARG 0.002 0.000 ARG A 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7199 (ttt90) REVERT: D 85 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6617 (mm) REVERT: B 701 MET cc_start: 0.6374 (mpp) cc_final: 0.5943 (mpp) outliers start: 42 outliers final: 36 residues processed: 183 average time/residue: 0.2975 time to fit residues: 92.1634 Evaluate side-chains 176 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 579 MET 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 D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.124443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077993 restraints weight = 44216.383| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.48 r_work: 0.2923 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22946 Z= 0.207 Angle : 0.593 11.835 31232 Z= 0.290 Chirality : 0.042 0.277 3528 Planarity : 0.004 0.040 3912 Dihedral : 4.591 58.991 3719 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.72 % Allowed : 20.38 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2700 helix: 1.08 (0.13), residues: 1626 sheet: -1.28 (0.81), residues: 42 loop : -1.93 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 481 HIS 0.004 0.001 HIS C 241 PHE 0.011 0.001 PHE B 546 TYR 0.019 0.001 TYR D 209 ARG 0.002 0.000 ARG C 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4512.52 seconds wall clock time: 82 minutes 49.24 seconds (4969.24 seconds total)