Starting phenix.real_space_refine on Thu Aug 8 06:45:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/08_2024/8i93_35256.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/08_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_35256/08_2024/8i93_35256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/08_2024/8i93_35256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/08_2024/8i93_35256.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i93_35256/08_2024/8i93_35256.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 13.44, per 1000 atoms: 0.60 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: 9.96 Conformation dependent library (CDL) restraints added in 4.0 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: 2.36 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: 6.81 Time building geometry restraints manager: 10.76 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 Time spend for trying shortcut: 0.00 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: 8.290 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: 0.000 Extract box with map and model: 1.290 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 64.790 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.470 ------------------------------------------------------------------------------- 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 : 2.527 Fit side-chains outliers start: 94 outliers final: 36 residues processed: 423 average time/residue: 0.2832 time to fit residues: 195.0019 Evaluate side-chains 188 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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: 4.9990 chunk 203 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 210 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 149 ASN A 159 ASN A 175 GLN A 239 HIS A 305 GLN A 340 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 149 ASN C 159 ASN C 175 GLN C 239 HIS C 305 GLN C 340 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 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: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22946 Z= 0.214 Angle : 0.667 8.732 31232 Z= 0.344 Chirality : 0.044 0.206 3528 Planarity : 0.005 0.042 3912 Dihedral : 8.001 59.821 3773 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 2.76 % Allowed : 15.90 % Favored : 81.34 % 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: -2.27 (0.15), residues: 2700 helix: -0.70 (0.13), residues: 1602 sheet: -1.10 (0.70), residues: 42 loop : -2.78 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 196 HIS 0.004 0.001 HIS C 378 PHE 0.022 0.002 PHE D 529 TYR 0.018 0.002 TYR C 83 ARG 0.004 0.001 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 256 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 190 time to evaluate : 2.428 Fit side-chains REVERT: A 62 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7494 (ptm) REVERT: A 661 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: A 757 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6550 (mt) REVERT: C 62 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7482 (ptm) REVERT: C 661 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: C 757 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6529 (mt) REVERT: B 701 MET cc_start: 0.6387 (mpt) cc_final: 0.6031 (mpt) REVERT: D 701 MET cc_start: 0.6408 (mpt) cc_final: 0.6043 (mpt) outliers start: 66 outliers final: 29 residues processed: 247 average time/residue: 0.2839 time to fit residues: 116.1404 Evaluate side-chains 193 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 2.367 ------------------------------------------------------------------------------- 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 347 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 661 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 55 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 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 343 VAL Chi-restraints excluded: chain C residue 347 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 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 306 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 263 optimal weight: 0.0010 chunk 217 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN B 527 ASN D 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22946 Z= 0.363 Angle : 0.669 8.105 31232 Z= 0.341 Chirality : 0.046 0.193 3528 Planarity : 0.004 0.039 3912 Dihedral : 6.993 58.057 3733 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 3.35 % Allowed : 17.07 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.15), residues: 2700 helix: -0.33 (0.13), residues: 1618 sheet: -1.04 (0.71), residues: 42 loop : -2.61 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 478 HIS 0.006 0.001 HIS C 265 PHE 0.019 0.002 PHE B 48 TYR 0.016 0.002 TYR D 209 ARG 0.006 0.001 ARG A 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 254 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 174 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 HIS cc_start: 0.9230 (OUTLIER) cc_final: 0.8527 (t-90) REVERT: A 661 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: C 62 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7535 (ptm) REVERT: C 401 HIS cc_start: 0.9244 (OUTLIER) cc_final: 0.8556 (t-90) REVERT: C 661 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8000 (mp10) outliers start: 80 outliers final: 38 residues processed: 244 average time/residue: 0.2793 time to fit residues: 114.3673 Evaluate side-chains 193 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 2.460 ------------------------------------------------------------------------------- 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 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 661 GLN 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 188 SER 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 541 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain C residue 62 MET 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 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 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 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 306 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 586 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.3010 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= 0.243 Angle : 0.605 8.943 31232 Z= 0.306 Chirality : 0.043 0.271 3528 Planarity : 0.004 0.039 3912 Dihedral : 6.310 59.045 3727 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 2.68 % Allowed : 18.74 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), residues: 2700 helix: 0.03 (0.13), residues: 1614 sheet: -1.22 (0.71), residues: 42 loop : -2.34 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.004 0.001 HIS C 241 PHE 0.014 0.001 PHE B 550 TYR 0.017 0.001 TYR B 209 ARG 0.005 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 223 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 159 time to evaluate : 2.429 Fit side-chains REVERT: A 661 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: C 62 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7461 (ttp) REVERT: C 661 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: B 701 MET cc_start: 0.7041 (mpt) cc_final: 0.6762 (mmp) REVERT: D 701 MET cc_start: 0.7053 (mpt) cc_final: 0.6762 (mmp) outliers start: 64 outliers final: 40 residues processed: 211 average time/residue: 0.2743 time to fit residues: 98.1138 Evaluate side-chains 186 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 409 SER 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 560 LEU Chi-restraints excluded: chain A residue 626 SER 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 42 MET 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 355 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 C residue 62 MET 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 409 SER 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 661 GLN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 306 VAL 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 545 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 0.0970 chunk 147 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 65 optimal weight: 0.4980 overall best weight: 1.0380 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22946 Z= 0.176 Angle : 0.569 8.798 31232 Z= 0.286 Chirality : 0.041 0.200 3528 Planarity : 0.004 0.040 3912 Dihedral : 5.809 59.847 3727 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 2.55 % Allowed : 18.66 % Favored : 78.79 % 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: -0.95 (0.16), residues: 2700 helix: 0.34 (0.13), residues: 1612 sheet: -1.41 (0.70), residues: 42 loop : -2.15 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.015 0.001 PHE B 546 TYR 0.010 0.001 TYR D 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 218 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 157 time to evaluate : 2.381 Fit side-chains REVERT: A 115 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7215 (ttt90) REVERT: C 115 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7216 (ttt90) REVERT: D 85 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6862 (mm) outliers start: 61 outliers final: 35 residues processed: 205 average time/residue: 0.2950 time to fit residues: 99.4270 Evaluate side-chains 180 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 2.637 ------------------------------------------------------------------------------- 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 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 626 SER 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 197 MET Chi-restraints excluded: chain B residue 198 LEU 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 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 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER 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 D residue 42 MET 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 582 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN D 8 ASN D 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22946 Z= 0.314 Angle : 0.622 7.844 31232 Z= 0.314 Chirality : 0.044 0.267 3528 Planarity : 0.004 0.039 3912 Dihedral : 5.638 59.481 3723 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 3.14 % Allowed : 18.41 % Favored : 78.45 % 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: -0.88 (0.16), residues: 2700 helix: 0.35 (0.13), residues: 1624 sheet: -1.15 (0.75), residues: 42 loop : -2.07 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 478 HIS 0.005 0.001 HIS A 265 PHE 0.014 0.001 PHE C 464 TYR 0.015 0.002 TYR C 385 ARG 0.008 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 221 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 146 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7270 (ttt90) REVERT: A 401 HIS cc_start: 0.9263 (OUTLIER) cc_final: 0.8565 (t-90) REVERT: A 559 ARG cc_start: 0.8071 (ppt90) cc_final: 0.7832 (ppt90) REVERT: C 115 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7271 (ttt90) REVERT: C 401 HIS cc_start: 0.9268 (OUTLIER) cc_final: 0.8573 (t-90) REVERT: C 762 PHE cc_start: 0.4499 (OUTLIER) cc_final: 0.3610 (t80) REVERT: D 85 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6786 (mm) outliers start: 75 outliers final: 48 residues processed: 214 average time/residue: 0.2974 time to fit residues: 105.4002 Evaluate side-chains 191 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 132 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER 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 560 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 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 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 448 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 545 ILE 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 132 VAL 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 401 HIS Chi-restraints excluded: chain C residue 409 SER 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 539 LEU 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 C residue 755 VAL Chi-restraints excluded: chain C residue 762 PHE Chi-restraints excluded: chain D residue 42 MET 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 306 VAL 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 448 VAL Chi-restraints excluded: chain D residue 485 LEU 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: 1.9990 chunk 29 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 218 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 258 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 119 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22946 Z= 0.156 Angle : 0.553 8.668 31232 Z= 0.278 Chirality : 0.041 0.212 3528 Planarity : 0.004 0.039 3912 Dihedral : 5.200 59.231 3723 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.18 % Allowed : 19.54 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2700 helix: 0.67 (0.13), residues: 1622 sheet: -1.47 (0.73), residues: 42 loop : -1.88 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.014 0.001 PHE B 550 TYR 0.014 0.001 TYR B 209 ARG 0.007 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: 52 poor density : 156 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7176 (ttt90) REVERT: A 559 ARG cc_start: 0.7999 (ppt90) cc_final: 0.7736 (ppt90) REVERT: C 115 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7177 (ttt90) outliers start: 52 outliers final: 33 residues processed: 199 average time/residue: 0.3042 time to fit residues: 101.2376 Evaluate side-chains 173 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 435 GLU 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 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 582 VAL 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 409 SER Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 520 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 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 197 MET 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 582 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 234 optimal weight: 0.0370 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN D 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22946 Z= 0.166 Angle : 0.551 9.719 31232 Z= 0.277 Chirality : 0.041 0.257 3528 Planarity : 0.004 0.039 3912 Dihedral : 4.778 59.051 3719 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.18 % Allowed : 19.41 % Favored : 78.41 % 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: -0.31 (0.16), residues: 2700 helix: 0.83 (0.13), residues: 1628 sheet: -1.78 (0.70), residues: 42 loop : -1.85 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE B 529 TYR 0.017 0.001 TYR D 209 ARG 0.005 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 199 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7161 (ttt90) REVERT: A 401 HIS cc_start: 0.9210 (OUTLIER) cc_final: 0.8589 (t-90) REVERT: A 559 ARG cc_start: 0.8082 (ppt90) cc_final: 0.7835 (ppt90) REVERT: C 115 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7162 (ttt90) REVERT: C 401 HIS cc_start: 0.9210 (OUTLIER) cc_final: 0.8589 (t-90) REVERT: D 85 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6863 (mm) outliers start: 52 outliers final: 37 residues processed: 192 average time/residue: 0.2876 time to fit residues: 92.3594 Evaluate side-chains 181 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 HIS Chi-restraints excluded: chain A residue 409 SER 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 560 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 B residue 55 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU 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 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER 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 692 SER Chi-restraints excluded: chain C residue 721 SER 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 197 MET 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 582 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.7951 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 0.040 22946 Z= 0.182 Angle : 0.564 9.841 31232 Z= 0.282 Chirality : 0.042 0.247 3528 Planarity : 0.004 0.039 3912 Dihedral : 4.703 59.554 3719 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.88 % Allowed : 19.75 % Favored : 78.37 % 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: -0.18 (0.16), residues: 2700 helix: 0.95 (0.13), residues: 1616 sheet: -1.58 (0.74), residues: 42 loop : -1.80 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 478 HIS 0.003 0.001 HIS A 241 PHE 0.014 0.001 PHE B 546 TYR 0.018 0.001 TYR B 209 ARG 0.006 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 188 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7173 (ttt90) REVERT: A 401 HIS cc_start: 0.9218 (OUTLIER) cc_final: 0.8599 (t-90) REVERT: A 559 ARG cc_start: 0.8065 (ppt90) cc_final: 0.7833 (ppt90) REVERT: C 115 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7174 (ttt90) REVERT: C 401 HIS cc_start: 0.9218 (OUTLIER) cc_final: 0.8597 (t-90) REVERT: D 85 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6785 (mm) REVERT: D 701 MET cc_start: 0.6990 (mmt) cc_final: 0.6786 (mmt) outliers start: 45 outliers final: 36 residues processed: 183 average time/residue: 0.2834 time to fit residues: 86.8313 Evaluate side-chains 177 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 136 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 HIS Chi-restraints excluded: chain A residue 409 SER 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 560 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU 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 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER 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 692 SER Chi-restraints excluded: chain C residue 721 SER 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 197 MET Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 485 LEU 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: 3.9990 chunk 155 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.3935 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= 0.216 Angle : 0.582 11.164 31232 Z= 0.290 Chirality : 0.042 0.258 3528 Planarity : 0.004 0.039 3912 Dihedral : 4.718 59.418 3719 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.88 % Allowed : 19.83 % Favored : 78.28 % 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: -0.15 (0.16), residues: 2700 helix: 0.99 (0.13), residues: 1616 sheet: -1.58 (0.74), residues: 42 loop : -1.81 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.004 0.001 HIS C 241 PHE 0.010 0.001 PHE A 464 TYR 0.016 0.001 TYR B 209 ARG 0.005 0.000 ARG C 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 191 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 2.360 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7259 (ttt90) REVERT: A 401 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8507 (t-90) REVERT: A 559 ARG cc_start: 0.8083 (ppt90) cc_final: 0.7877 (ppt90) REVERT: C 115 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7259 (ttt90) REVERT: C 401 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8507 (t-90) REVERT: D 85 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7317 (mm) REVERT: B 701 MET cc_start: 0.7061 (mmt) cc_final: 0.6755 (mmt) REVERT: D 701 MET cc_start: 0.7017 (mmt) cc_final: 0.6782 (mmt) outliers start: 45 outliers final: 33 residues processed: 186 average time/residue: 0.3058 time to fit residues: 95.1264 Evaluate side-chains 175 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 HIS Chi-restraints excluded: chain A residue 409 SER 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 560 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 B residue 42 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU 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 347 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER 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 692 SER Chi-restraints excluded: chain C residue 721 SER 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 422 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4766 > 50: distance: 68 - 118: 26.678 distance: 81 - 86: 28.908 distance: 82 - 104: 32.065 distance: 86 - 87: 26.937 distance: 87 - 88: 6.290 distance: 87 - 90: 32.399 distance: 88 - 89: 7.422 distance: 89 - 113: 53.300 distance: 90 - 91: 39.656 distance: 91 - 92: 40.097 distance: 91 - 93: 41.273 distance: 94 - 95: 40.784 distance: 95 - 96: 28.639 distance: 96 - 97: 40.911 distance: 96 - 104: 40.602 distance: 98 - 99: 20.474 distance: 99 - 100: 30.678 distance: 99 - 101: 43.923 distance: 100 - 102: 32.688 distance: 101 - 103: 32.445 distance: 102 - 103: 27.126 distance: 104 - 105: 27.618 distance: 105 - 106: 31.981 distance: 105 - 108: 36.294 distance: 106 - 107: 34.622 distance: 106 - 113: 34.568 distance: 108 - 109: 11.791 distance: 109 - 110: 33.259 distance: 110 - 111: 27.780 distance: 111 - 112: 27.750 distance: 113 - 114: 23.964 distance: 114 - 115: 24.402 distance: 114 - 117: 34.920 distance: 115 - 116: 8.258 distance: 115 - 119: 31.110 distance: 117 - 118: 8.239 distance: 119 - 120: 14.297 distance: 120 - 121: 15.734 distance: 120 - 123: 41.392 distance: 121 - 122: 55.411 distance: 121 - 127: 40.693 distance: 123 - 124: 39.696 distance: 124 - 125: 40.602 distance: 127 - 128: 5.313 distance: 128 - 129: 3.158 distance: 128 - 131: 40.711 distance: 129 - 130: 4.790 distance: 129 - 135: 38.440 distance: 131 - 132: 5.931 distance: 131 - 133: 25.121 distance: 132 - 134: 5.751 distance: 135 - 136: 55.506 distance: 136 - 137: 27.685 distance: 136 - 139: 18.402 distance: 137 - 141: 4.363 distance: 141 - 142: 19.209 distance: 142 - 143: 25.921 distance: 142 - 145: 13.456 distance: 143 - 149: 46.372 distance: 145 - 146: 3.439 distance: 146 - 147: 22.887 distance: 146 - 148: 10.696 distance: 148 - 205: 22.742 distance: 149 - 150: 37.632 distance: 150 - 151: 41.071 distance: 150 - 153: 55.568 distance: 151 - 152: 39.015 distance: 155 - 156: 12.152 distance: 156 - 157: 27.844 distance: 156 - 159: 38.361 distance: 157 - 158: 13.888 distance: 157 - 162: 10.035 distance: 158 - 180: 23.239 distance: 159 - 160: 21.331 distance: 159 - 161: 11.630