Starting phenix.real_space_refine on Sun Aug 11 04:22:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y88_39037/08_2024/8y88_39037.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y88_39037/08_2024/8y88_39037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y88_39037/08_2024/8y88_39037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y88_39037/08_2024/8y88_39037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y88_39037/08_2024/8y88_39037.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y88_39037/08_2024/8y88_39037.cif" } resolution = 3.03 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 194 5.16 5 C 19941 2.51 5 N 5094 2.21 5 O 6028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31257 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9152 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1127} Chain breaks: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 9037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9037 Classifications: {'peptide': 1179} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1122} Chain breaks: 5 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 9239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9239 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "T" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1727 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "I" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1727 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 17.39, per 1000 atoms: 0.56 Number of scatterers: 31257 At special positions: 0 Unit cell: (156.62, 137.76, 240.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 194 16.00 O 6028 8.00 N 5094 7.00 C 19941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=75, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 476 " distance=2.02 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 495 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS T 410 " - pdb=" SG CYS T 426 " distance=2.03 Simple disulfide: pdb=" SG CYS T 437 " - pdb=" SG CYS T 465 " distance=2.03 Simple disulfide: pdb=" SG CYS I 410 " - pdb=" SG CYS I 426 " distance=2.03 Simple disulfide: pdb=" SG CYS I 437 " - pdb=" SG CYS I 465 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 703 " " NAG A1302 " - " ASN A 335 " " NAG A1303 " - " ASN A 664 " " NAG A1304 " - " ASN A 725 " " NAG A1305 " - " ASN A 793 " " NAG A1306 " - " ASN A1211 " " NAG A1307 " - " ASN A 192 " " NAG A1308 " - " ASN A 58 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 192 " " NAG B1303 " - " ASN B 725 " " NAG B1304 " - " ASN B1211 " " NAG B1305 " - " ASN B 664 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 703 " " NAG C1303 " - " ASN C 664 " " NAG C1304 " - " ASN C 793 " " NAG C1305 " - " ASN C 192 " " NAG D 1 " - " ASN A 188 " " NAG E 1 " - " ASN C 132 " " NAG F 1 " - " ASN C 188 " " NAG G 1 " - " ASN B 188 " Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 6.3 seconds 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7566 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 71 sheets defined 21.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.714A pdb=" N ASN A 115 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.536A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.673A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.623A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.832A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.067A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.138A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.640A pdb=" N VAL A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.876A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.575A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.813A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.916A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 3.555A pdb=" N GLN A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 966 removed outlier: 3.615A pdb=" N ALA A 961 " --> pdb=" O GLY A 957 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 990 removed outlier: 4.178A pdb=" N GLN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 998 removed outlier: 3.898A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.573A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.597A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.546A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1113 removed outlier: 3.789A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.672A pdb=" N TYR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.749A pdb=" N LEU C 333 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN C 335 " --> pdb=" O TRP C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.753A pdb=" N LEU C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.565A pdb=" N ILE C 378 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 379' Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.512A pdb=" N VAL C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 478 through 483' Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 removed outlier: 4.192A pdb=" N ASN C 702 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.558A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 862 removed outlier: 3.579A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 901 through 909 removed outlier: 3.928A pdb=" N LEU C 906 " --> pdb=" O PRO C 902 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.944A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 940 Processing helix chain 'C' and resid 953 through 965 removed outlier: 3.643A pdb=" N ALA C 962 " --> pdb=" O TYR C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.830A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1018 removed outlier: 3.504A pdb=" N ILE C1004 " --> pdb=" O ASN C1000 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C1005 " --> pdb=" O GLN C1001 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1046 removed outlier: 3.871A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN C1036 " --> pdb=" O VAL C1032 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.588A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.642A pdb=" N ILE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.053A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.733A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.571A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 485 " --> pdb=" O VAL B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 485' Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.678A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.623A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 836 through 863 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.740A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.881A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 removed outlier: 3.699A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 940 " --> pdb=" O CYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 964 removed outlier: 3.539A pdb=" N ALA B 961 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.946A pdb=" N PHE B 968 " --> pdb=" O ALA B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.700A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 removed outlier: 3.518A pdb=" N ASN B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.523A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.654A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1065 removed outlier: 3.556A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 4.361A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B1093 " --> pdb=" O VAL B1089 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'T' and resid 299 through 303 Processing helix chain 'T' and resid 406 through 411 Processing helix chain 'T' and resid 480 through 492 Processing helix chain 'I' and resid 299 through 303 Processing helix chain 'I' and resid 406 through 411 Processing helix chain 'I' and resid 480 through 492 removed outlier: 3.842A pdb=" N GLY I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.471A pdb=" N VAL A 55 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 658 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 67 removed outlier: 3.686A pdb=" N SER A 262 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLN A 265 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP A 281 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.442A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.772A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 226 removed outlier: 5.203A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.738A pdb=" N TYR A 692 " --> pdb=" O CYS A 719 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 719 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 319 removed outlier: 3.795A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 622 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 629 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 648 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.503A pdb=" N ARG A 347 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 388 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 424 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE A 368 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB2, first strand: chain 'A' and resid 461 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AB4, first strand: chain 'A' and resid 556 through 557 removed outlier: 4.084A pdb=" N PHE A 566 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.521A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.035A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 786 through 791 Processing sheet with id=AB8, first strand: chain 'A' and resid 794 through 803 Processing sheet with id=AB9, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.450A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 944 " --> pdb=" O THR A 811 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.620A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 878 through 879 removed outlier: 3.508A pdb=" N VAL A 879 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1162 through 1163 Processing sheet with id=AC4, first strand: chain 'A' and resid 1169 through 1172 Processing sheet with id=AC5, first strand: chain 'A' and resid 1175 through 1179 Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 67 removed outlier: 3.697A pdb=" N SER C 262 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.611A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.573A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 148 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 110 through 112 Processing sheet with id=AD1, first strand: chain 'C' and resid 155 through 160 removed outlier: 10.942A pdb=" N TYR C 158 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N HIS C 175 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS C 160 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 173 " --> pdb=" O HIS C 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 302 through 305 removed outlier: 3.713A pdb=" N TYR C 692 " --> pdb=" O CYS C 719 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS C 719 " --> pdb=" O TYR C 692 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 309 through 310 removed outlier: 3.509A pdb=" N PHE C 309 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 675 " --> pdb=" O PHE C 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AD5, first strand: chain 'C' and resid 346 through 349 removed outlier: 4.026A pdb=" N ARG C 347 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 388 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 595 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 387 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 427 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 592 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 382 through 383 Processing sheet with id=AD7, first strand: chain 'C' and resid 459 through 463 removed outlier: 3.984A pdb=" N SER C 576 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.821A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AE1, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.523A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 619 through 620 removed outlier: 3.947A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.230A pdb=" N ASN C 725 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 764 " --> pdb=" O ASN C 725 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR C 766 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR C 729 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 736 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.080A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 786 through 803 removed outlier: 7.007A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.480A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 944 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.532A pdb=" N GLY C1169 " --> pdb=" O MET C1205 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AE9, first strand: chain 'B' and resid 35 through 39 removed outlier: 8.078A pdb=" N SER B 36 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASP B 76 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP B 38 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 74 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 211 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 63 through 67 Processing sheet with id=AF2, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.725A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 140 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 109 through 113 removed outlier: 3.952A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.701A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AF6, first strand: chain 'B' and resid 317 through 319 removed outlier: 7.455A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 631 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AF8, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.616A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 388 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER B 422 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N CYS B 370 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLN B 424 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 368 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.616A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 388 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AG2, first strand: chain 'B' and resid 459 through 463 removed outlier: 3.521A pdb=" N TYR B 462 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.785A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AG5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.893A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 573 " --> pdb=" O GLY B 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'B' and resid 730 through 731 removed outlier: 6.883A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 786 through 791 removed outlier: 7.219A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 794 through 795 Processing sheet with id=AG9, first strand: chain 'B' and resid 798 through 803 removed outlier: 3.544A pdb=" N ALA B1137 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.398A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 1202 through 1204 Processing sheet with id=AH3, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.276A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU T 378 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER T 448 " --> pdb=" O LEU T 378 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL T 446 " --> pdb=" O TRP T 380 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER T 382 " --> pdb=" O PRO T 444 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY T 457 " --> pdb=" O PRO T 444 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 452 through 453 removed outlier: 3.601A pdb=" N LYS T 449 " --> pdb=" O ILE T 452 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER T 382 " --> pdb=" O PRO T 444 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL T 446 " --> pdb=" O TRP T 380 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER T 448 " --> pdb=" O LEU T 378 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU T 378 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS T 426 " --> pdb=" O ILE T 405 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE T 425 " --> pdb=" O TYR T 474 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR T 474 " --> pdb=" O ILE T 425 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 278 through 283 removed outlier: 5.034A pdb=" N HIS T 279 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL T 275 " --> pdb=" O HIS T 279 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS T 281 " --> pdb=" O LEU T 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER T 272 " --> pdb=" O PHE T 311 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS T 330 " --> pdb=" O LYS T 350 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 260 through 261 removed outlier: 4.330A pdb=" N ASN I 398 " --> pdb=" O GLY I 383 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY I 383 " --> pdb=" O ASN I 398 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU I 378 " --> pdb=" O SER I 448 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER I 448 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL I 446 " --> pdb=" O TRP I 380 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER I 382 " --> pdb=" O PRO I 444 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS I 449 " --> pdb=" O ILE I 452 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 260 through 261 removed outlier: 4.452A pdb=" N CYS I 426 " --> pdb=" O ILE I 405 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLY I 457 " --> pdb=" O PRO I 444 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY I 442 " --> pdb=" O THR I 459 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS I 449 " --> pdb=" O ILE I 452 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 278 through 283 removed outlier: 5.053A pdb=" N HIS I 279 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL I 275 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS I 281 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 272 " --> pdb=" O PHE I 311 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS I 330 " --> pdb=" O LYS I 350 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2586 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: 15.11 Time building geometry restraints manager: 13.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9940 1.34 - 1.46: 7852 1.46 - 1.58: 14004 1.58 - 1.70: 0 1.70 - 1.81: 229 Bond restraints: 32025 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 32020 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.25: 1069 107.25 - 113.94: 17911 113.94 - 120.63: 11956 120.63 - 127.32: 12462 127.32 - 134.02: 309 Bond angle restraints: 43707 Sorted by residual: angle pdb=" N ILE A 656 " pdb=" CA ILE A 656 " pdb=" C ILE A 656 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" C ALA A 392 " pdb=" N ILE A 393 " pdb=" CA ILE A 393 " ideal model delta sigma weight residual 122.13 126.74 -4.61 1.85e+00 2.92e-01 6.20e+00 angle pdb=" CA GLY T 462 " pdb=" C GLY T 462 " pdb=" N SER T 463 " ideal model delta sigma weight residual 114.58 116.71 -2.13 8.60e-01 1.35e+00 6.15e+00 angle pdb=" N VAL B 482 " pdb=" CA VAL B 482 " pdb=" C VAL B 482 " ideal model delta sigma weight residual 113.07 109.79 3.28 1.36e+00 5.41e-01 5.82e+00 angle pdb=" N PRO B1067 " pdb=" CA PRO B1067 " pdb=" C PRO B1067 " ideal model delta sigma weight residual 110.70 113.56 -2.86 1.22e+00 6.72e-01 5.49e+00 ... (remaining 43702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 18970 21.80 - 43.60: 332 43.60 - 65.40: 37 65.40 - 87.20: 9 87.20 - 109.00: 4 Dihedral angle restraints: 19352 sinusoidal: 7575 harmonic: 11777 Sorted by residual: dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 495 " pdb=" CB CYS A 495 " ideal model delta sinusoidal sigma weight residual -86.00 -4.56 -81.44 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 495 " pdb=" SG CYS A 495 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -151.72 65.72 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 476 " pdb=" CB CYS A 476 " ideal model delta sinusoidal sigma weight residual -86.00 -150.68 64.68 1 1.00e+01 1.00e-02 5.49e+01 ... (remaining 19349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4291 0.055 - 0.109: 663 0.109 - 0.164: 81 0.164 - 0.219: 0 0.219 - 0.273: 1 Chirality restraints: 5036 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE A 393 " pdb=" CA ILE A 393 " pdb=" CG1 ILE A 393 " pdb=" CG2 ILE A 393 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" C2 BMA E 3 " pdb=" C1 BMA E 3 " pdb=" C3 BMA E 3 " pdb=" O2 BMA E 3 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 5033 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1067 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO B1068 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B1068 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B1068 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B1067 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C1067 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " -0.019 5.00e-02 4.00e+02 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2709 2.75 - 3.29: 29656 3.29 - 3.82: 47811 3.82 - 4.36: 55404 4.36 - 4.90: 98860 Nonbonded interactions: 234440 Sorted by model distance: nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.210 3.040 nonbonded pdb=" O VAL C 113 " pdb=" OG1 THR C 116 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASN A 351 " pdb=" OG1 THR A 601 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP C 507 " pdb=" OG SER I 463 " model vdw 2.259 3.040 nonbonded pdb=" O TRP C 89 " pdb=" OH TYR C 236 " model vdw 2.265 3.040 ... (remaining 234435 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' and (resid 14 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 or (resid 26 and (name N or name CA or nam \ e C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or n \ ame C or name O or name CB )) or resid 29 or (resid 30 through 31 and (name N or \ name CA or name C or name O or name CB )) or resid 32 through 83 or (resid 84 a \ nd (name N or name CA or name C or name O or name CB )) or resid 85 through 242 \ or (resid 243 through 245 and (name N or name CA or name C or name O or name CB \ )) or resid 246 through 359 or (resid 360 through 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 or (resid 364 and (name N or name CA \ or name C or name O or name CB )) or resid 365 through 370 or (resid 371 throug \ h 375 and (name N or name CA or name C or name O or name CB )) or resid 376 or ( \ resid 377 and (name N or name CA or name C or name O or name CB )) or resid 378 \ through 395 or (resid 396 through 402 and (name N or name CA or name C or name O \ or name CB )) or (resid 408 and (name N or name CA or name C or name O or name \ CB )) or resid 409 or (resid 410 and (name N or name CA or name C or name O or n \ ame CB )) or resid 411 or (resid 412 through 413 and (name N or name CA or name \ C or name O or name CB )) or resid 422 through 430 or (resid 431 through 432 and \ (name N or name CA or name C or name O or name CB )) or resid 433 through 436 o \ r (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 38 through 446 or resid 449 through 461 or (resid 462 through 465 and (name N or \ name CA or name C or name O or name CB )) or resid 466 through 491 or (resid 49 \ 2 through 493 and (name N or name CA or name C or name O or name CB )) or resid \ 494 through 557 or resid 563 through 584 or (resid 585 and (name N or name CA or \ name C or name O or name CB )) or resid 586 through 608 or (resid 609 and (name \ N or name CA or name C or name O or name CB )) or resid 610 through 615 or (res \ id 616 and (name N or name CA or name C or name O or name CB )) or resid 617 thr \ ough 619 or (resid 620 and (name N or name CA or name C or name O or name CB )) \ or resid 621 through 629 or (resid 630 and (name N or name CA or name C or name \ O or name CB )) or resid 631 or (resid 632 and (name N or name CA or name C or n \ ame O or name CB )) or resid 633 or (resid 634 and (name N or name CA or name C \ or name O or name CB )) or resid 635 through 651 or (resid 652 and (name N or na \ me CA or name C or name O or name CB )) or resid 653 or (resid 654 and (name N o \ r name CA or name C or name O or name CB )) or resid 655 through 659 or (resid 6 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 661 through \ 708 or (resid 709 and (name N or name CA or name C or name O or name CB )) or r \ esid 710 through 779 or (resid 780 and (name N or name CA or name C or name O or \ name CB )) or resid 781 through 871 or (resid 872 and (name N or name CA or nam \ e C or name O or name CB )) or resid 873 or (resid 874 and (name N or name CA or \ name C or name O or name CB )) or resid 875 or (resid 876 and (name N or name C \ A or name C or name O or name CB )) or resid 877 through 893 or (resid 894 and ( \ name N or name CA or name C or name O or name CB )) or resid 895 through 929 or \ (resid 930 through 932 and (name N or name CA or name C or name O or name CB )) \ or resid 933 through 951 or (resid 952 and (name N or name CA or name C or name \ O or name CB )) or resid 953 through 998 or (resid 999 and (name N or name CA or \ name C or name O or name CB )) or resid 1000 through 1148 or (resid 1149 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1150 through 1199 or \ (resid 1200 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 201 through 1221 or resid 1301 through 1305)) selection = (chain 'B' and (resid 14 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 72 or (resid 73 and (name N or nam \ e CA or name C or name O or name CB )) or resid 74 through 81 or (resid 82 and ( \ name N or name CA or name C or name O or name CB )) or resid 83 through 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 157 or (resid 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 163 or (resid 164 through 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 168 or (resid 169 and (name N o \ r name CA or name C or name O or name CB )) or resid 170 through 205 or (resid 2 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 207 through \ 244 or (resid 245 and (name N or name CA or name C or name O or name CB )) or r \ esid 246 through 359 or (resid 360 through 362 and (name N or name CA or name C \ or name O or name CB )) or resid 363 or (resid 364 and (name N or name CA or nam \ e C or name O or name CB )) or resid 365 through 370 or (resid 371 through 375 a \ nd (name N or name CA or name C or name O or name CB )) or resid 376 or (resid 3 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 378 through \ 395 or (resid 396 through 402 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 408 and (name N or name CA or name C or name O or name CB )) o \ r resid 409 or (resid 410 and (name N or name CA or name C or name O or name CB \ )) or resid 411 or (resid 412 through 413 and (name N or name CA or name C or na \ me O or name CB )) or resid 422 through 430 or (resid 431 through 432 and (name \ N or name CA or name C or name O or name CB )) or resid 433 through 436 or (resi \ d 437 and (name N or name CA or name C or name O or name CB )) or resid 438 thro \ ugh 446 or resid 449 through 461 or (resid 462 through 465 and (name N or name C \ A or name C or name O or name CB )) or resid 466 through 469 or (resid 470 and ( \ name N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 a \ nd (name N or name CA or name C or name O or name CB )) or resid 473 through 501 \ or (resid 502 and (name N or name CA or name C or name O or name CB )) or resid \ 503 or (resid 515 and (name N or name CA or name C or name O or name CB )) or r \ esid 516 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 584 or (resid 585 and (name N or name CA or \ name C or name O or name CB )) or resid 586 through 608 or (resid 609 and (name \ N or name CA or name C or name O or name CB )) or resid 610 through 659 or (res \ id 660 and (name N or name CA or name C or name O or name CB )) or resid 661 thr \ ough 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 708 or (resid 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 through 779 or (resid 780 and (name N or name CA or \ name C or name O or name CB )) or resid 781 through 871 or (resid 872 and (name \ N or name CA or name C or name O or name CB )) or resid 873 or (resid 874 and ( \ name N or name CA or name C or name O or name CB )) or resid 875 through 893 or \ (resid 894 and (name N or name CA or name C or name O or name CB )) or resid 895 \ through 931 or (resid 932 and (name N or name CA or name C or name O or name CB \ )) or resid 933 through 951 or (resid 952 and (name N or name CA or name C or n \ ame O or name CB )) or resid 953 through 998 or (resid 999 and (name N or name C \ A or name C or name O or name CB )) or resid 1000 through 1199 or (resid 1200 an \ d (name N or name CA or name C or name O or name CB )) or resid 1201 through 122 \ 1 or resid 1301 through 1305)) selection = (chain 'C' and (resid 14 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 or (resid 26 and (name N or name CA or nam \ e C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or n \ ame C or name O or name CB )) or resid 29 through 30 or (resid 31 and (name N or \ name CA or name C or name O or name CB )) or resid 32 through 68 or (resid 69 a \ nd (name N or name CA or name C or name O or name CB )) or resid 70 through 72 o \ r (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 \ through 81 or (resid 82 and (name N or name CA or name C or name O or name CB ) \ ) or resid 83 or (resid 84 and (name N or name CA or name C or name O or name CB \ )) or resid 85 through 90 or (resid 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 through 157 or (resid 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 through 163 or (resid 164 through 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 205 or (resid 206 and (name N or name CA or name C or name O or \ name CB )) or resid 207 through 217 or (resid 218 and (name N or name CA or nam \ e C or name O or name CB )) or resid 219 through 242 or (resid 243 through 245 a \ nd (name N or name CA or name C or name O or name CB )) or resid 246 through 311 \ or (resid 312 and (name N or name CA or name C or name O or name CB )) or resid \ 313 through 469 or (resid 470 and (name N or name CA or name C or name O or nam \ e CB )) or resid 471 or (resid 472 and (name N or name CA or name C or name O or \ name CB )) or resid 473 through 501 or (resid 502 and (name N or name CA or nam \ e C or name O or name CB )) or resid 503 or (resid 515 and (name N or name CA or \ name C or name O or name CB )) or resid 516 through 520 or (resid 521 and (name \ N or name CA or name C or name O or name CB )) or resid 522 or (resid 523 and ( \ name N or name CA or name C or name O or name CB )) or resid 524 through 615 or \ (resid 616 and (name N or name CA or name C or name O or name CB )) or resid 617 \ through 619 or (resid 620 and (name N or name CA or name C or name O or name CB \ )) or resid 621 through 629 or (resid 630 and (name N or name CA or name C or n \ ame O or name CB )) or resid 631 or (resid 632 and (name N or name CA or name C \ or name O or name CB )) or resid 633 through 651 or (resid 652 and (name N or na \ me CA or name C or name O or name CB )) or resid 653 or (resid 654 and (name N o \ r name CA or name C or name O or name CB )) or resid 655 through 705 or (resid 7 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 707 through \ 875 or (resid 876 and (name N or name CA or name C or name O or name CB )) or r \ esid 877 through 930 or (resid 931 through 932 and (name N or name CA or name C \ or name O or name CB )) or resid 933 through 1148 or (resid 1149 and (name N or \ name CA or name C or name O or name CB )) or resid 1150 through 1221 or resid 13 \ 01 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'T' } 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: 3.060 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: 0.040 Extract box with map and model: 1.130 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 86.880 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.002 0.046 32025 Z= 0.134 Angle : 0.414 6.324 43707 Z= 0.217 Chirality : 0.041 0.273 5036 Planarity : 0.003 0.067 5600 Dihedral : 7.750 109.005 11561 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.72 % Allowed : 4.05 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -3.28 (0.11), residues: 4001 helix: -3.45 (0.10), residues: 715 sheet: -0.85 (0.18), residues: 757 loop : -2.33 (0.11), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 344 HIS 0.002 0.000 HIS C 826 PHE 0.006 0.001 PHE A 121 TYR 0.006 0.001 TYR C 649 ARG 0.002 0.000 ARG B 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 808 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 147 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6461 (tm-30) REVERT: A 160 HIS cc_start: 0.7694 (p90) cc_final: 0.7391 (p90) REVERT: A 266 TYR cc_start: 0.8063 (m-80) cc_final: 0.7811 (m-80) REVERT: A 277 THR cc_start: 0.8784 (m) cc_final: 0.8304 (p) REVERT: A 415 LYS cc_start: 0.8424 (tttm) cc_final: 0.8213 (ttpp) REVERT: A 439 PHE cc_start: 0.8106 (t80) cc_final: 0.7801 (t80) REVERT: A 500 LYS cc_start: 0.7998 (pptt) cc_final: 0.7557 (pptt) REVERT: A 632 ILE cc_start: 0.8355 (mt) cc_final: 0.8025 (mp) REVERT: A 646 ASN cc_start: 0.6949 (p0) cc_final: 0.6644 (p0) REVERT: A 669 ILE cc_start: 0.8530 (mt) cc_final: 0.8325 (mt) REVERT: A 670 LEU cc_start: 0.7773 (mp) cc_final: 0.7495 (mp) REVERT: A 801 GLU cc_start: 0.7019 (tt0) cc_final: 0.6715 (tt0) REVERT: A 884 PHE cc_start: 0.7550 (m-10) cc_final: 0.7024 (m-10) REVERT: A 998 ASN cc_start: 0.7792 (m110) cc_final: 0.7576 (m110) REVERT: A 1010 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8208 (ttmm) REVERT: A 1036 ASN cc_start: 0.8143 (t0) cc_final: 0.7926 (t0) REVERT: A 1095 ASP cc_start: 0.7459 (t0) cc_final: 0.7200 (t0) REVERT: A 1147 SER cc_start: 0.8369 (p) cc_final: 0.8115 (m) REVERT: A 1214 LYS cc_start: 0.7879 (mptp) cc_final: 0.7573 (mptp) REVERT: C 17 ASP cc_start: 0.7277 (m-30) cc_final: 0.7050 (m-30) REVERT: C 66 TYR cc_start: 0.8421 (m-80) cc_final: 0.8209 (m-80) REVERT: C 712 TYR cc_start: 0.8083 (p90) cc_final: 0.7783 (p90) REVERT: C 851 ASP cc_start: 0.7099 (m-30) cc_final: 0.6857 (m-30) REVERT: C 883 ASP cc_start: 0.7868 (t70) cc_final: 0.7582 (t0) REVERT: C 885 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8063 (ttpp) REVERT: C 949 ILE cc_start: 0.8139 (mt) cc_final: 0.7702 (mt) REVERT: C 1156 VAL cc_start: 0.8472 (p) cc_final: 0.8216 (m) REVERT: B 114 ASN cc_start: 0.8157 (t0) cc_final: 0.7928 (t0) REVERT: B 142 HIS cc_start: 0.7386 (m-70) cc_final: 0.7120 (m-70) REVERT: B 146 LEU cc_start: 0.8355 (mt) cc_final: 0.8153 (mt) REVERT: B 161 THR cc_start: 0.7951 (t) cc_final: 0.7660 (m) REVERT: B 186 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7779 (mtmt) REVERT: B 334 ASN cc_start: 0.7632 (t0) cc_final: 0.7245 (t0) REVERT: B 614 ILE cc_start: 0.7145 (pt) cc_final: 0.6643 (pt) REVERT: B 623 ASP cc_start: 0.7957 (t0) cc_final: 0.7697 (t0) REVERT: B 636 VAL cc_start: 0.8546 (p) cc_final: 0.8282 (t) REVERT: B 655 ILE cc_start: 0.8265 (tt) cc_final: 0.7889 (tt) REVERT: B 660 ASP cc_start: 0.7638 (t0) cc_final: 0.7307 (t70) REVERT: B 812 ILE cc_start: 0.8323 (mt) cc_final: 0.8097 (mm) REVERT: B 1028 LYS cc_start: 0.8250 (mttt) cc_final: 0.7980 (mtpp) REVERT: B 1060 GLU cc_start: 0.7533 (tt0) cc_final: 0.7254 (tt0) REVERT: B 1066 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6872 (p0) REVERT: B 1114 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7343 (m) REVERT: B 1120 ARG cc_start: 0.8454 (mtp180) cc_final: 0.8103 (mtp180) REVERT: B 1170 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8350 (pt) REVERT: B 1198 SER cc_start: 0.8200 (p) cc_final: 0.7744 (m) REVERT: T 405 ILE cc_start: 0.4694 (pt) cc_final: 0.4371 (pt) outliers start: 59 outliers final: 19 residues processed: 850 average time/residue: 0.4007 time to fit residues: 548.6479 Evaluate side-chains 653 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 630 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 2.9990 chunk 303 optimal weight: 0.0770 chunk 168 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 313 optimal weight: 0.1980 chunk 121 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 363 optimal weight: 7.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 175 HIS A 204 GLN A 291 GLN A 353 ASN A 364 HIS A 445 ASN A 598 ASN A 605 ASN A 709 GLN A 722 ASN A 840 ASN A 847 ASN A 941 ASN A1135 GLN C 171 ASN C 265 GLN C 440 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 954 GLN C 988 ASN C 998 ASN C1038 GLN C1041 ASN C1046 GLN C1071 GLN C1111 ASN C1201 ASN B 29 ASN B 204 GLN B 646 ASN B 840 ASN B 856 GLN B1073 GLN B1092 GLN T 276 GLN T 334 HIS I 276 GLN I 476 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32025 Z= 0.203 Angle : 0.541 15.606 43707 Z= 0.286 Chirality : 0.044 0.305 5036 Planarity : 0.004 0.078 5600 Dihedral : 5.453 67.271 4905 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.45 % Allowed : 10.07 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.88 (0.12), residues: 4001 helix: -0.22 (0.18), residues: 740 sheet: -0.30 (0.18), residues: 797 loop : -2.01 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 444 HIS 0.006 0.001 HIS B 201 PHE 0.033 0.001 PHE A 713 TYR 0.021 0.001 TYR C 212 ARG 0.006 0.000 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 633 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 51 VAL cc_start: 0.7578 (t) cc_final: 0.6734 (p) REVERT: A 147 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6499 (tm-30) REVERT: A 160 HIS cc_start: 0.7652 (p90) cc_final: 0.7328 (p90) REVERT: A 266 TYR cc_start: 0.8268 (m-80) cc_final: 0.7831 (m-80) REVERT: A 289 GLU cc_start: 0.7247 (tp30) cc_final: 0.7034 (tp30) REVERT: A 365 VAL cc_start: 0.8882 (p) cc_final: 0.8658 (m) REVERT: A 439 PHE cc_start: 0.8178 (t80) cc_final: 0.7890 (t80) REVERT: A 463 SER cc_start: 0.8358 (m) cc_final: 0.8083 (t) REVERT: A 464 ASP cc_start: 0.7542 (t0) cc_final: 0.7334 (t70) REVERT: A 500 LYS cc_start: 0.8038 (pptt) cc_final: 0.7503 (pptt) REVERT: A 537 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8125 (mtpp) REVERT: A 625 TYR cc_start: 0.7843 (m-10) cc_final: 0.7630 (m-10) REVERT: A 632 ILE cc_start: 0.8625 (mt) cc_final: 0.8312 (mp) REVERT: A 646 ASN cc_start: 0.7191 (p0) cc_final: 0.6906 (p0) REVERT: A 670 LEU cc_start: 0.8118 (mp) cc_final: 0.7814 (mt) REVERT: A 838 ASN cc_start: 0.7715 (m110) cc_final: 0.7357 (m110) REVERT: A 863 GLN cc_start: 0.7815 (tt0) cc_final: 0.7586 (tt0) REVERT: A 884 PHE cc_start: 0.7601 (m-10) cc_final: 0.7361 (m-10) REVERT: A 1010 LYS cc_start: 0.8273 (ttmm) cc_final: 0.8030 (ttmm) REVERT: A 1095 ASP cc_start: 0.7458 (t0) cc_final: 0.7203 (t0) REVERT: C 238 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8249 (mtm) REVERT: C 614 ILE cc_start: 0.8454 (mm) cc_final: 0.7896 (mt) REVERT: C 845 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: C 848 ASP cc_start: 0.7261 (m-30) cc_final: 0.6896 (m-30) REVERT: C 883 ASP cc_start: 0.7851 (t70) cc_final: 0.7642 (t0) REVERT: C 885 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7975 (ttpp) REVERT: C 1031 SER cc_start: 0.8309 (m) cc_final: 0.7966 (p) REVERT: C 1069 GLU cc_start: 0.7472 (tp30) cc_final: 0.7222 (tp30) REVERT: C 1075 ASP cc_start: 0.7156 (t0) cc_final: 0.6654 (t0) REVERT: C 1092 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7905 (mm-40) REVERT: C 1156 VAL cc_start: 0.8554 (p) cc_final: 0.8261 (m) REVERT: B 76 ASP cc_start: 0.6937 (t0) cc_final: 0.6655 (t70) REVERT: B 114 ASN cc_start: 0.8147 (t0) cc_final: 0.7920 (t0) REVERT: B 142 HIS cc_start: 0.7438 (m-70) cc_final: 0.7232 (m-70) REVERT: B 155 MET cc_start: 0.6183 (mmm) cc_final: 0.5891 (mmm) REVERT: B 258 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.7986 (p) REVERT: B 320 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7674 (ttm-80) REVERT: B 334 ASN cc_start: 0.7732 (t0) cc_final: 0.7311 (t0) REVERT: B 655 ILE cc_start: 0.8313 (tt) cc_final: 0.7871 (tt) REVERT: B 786 PHE cc_start: 0.7718 (m-80) cc_final: 0.7334 (m-80) REVERT: B 1028 LYS cc_start: 0.8266 (mttt) cc_final: 0.8006 (mtpp) REVERT: B 1060 GLU cc_start: 0.7346 (tt0) cc_final: 0.7130 (tt0) REVERT: B 1076 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7406 (mtt90) REVERT: B 1114 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7727 (m) REVERT: B 1131 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7930 (mp) REVERT: B 1170 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8175 (pt) REVERT: B 1195 GLU cc_start: 0.7767 (pt0) cc_final: 0.7565 (pt0) REVERT: T 405 ILE cc_start: 0.4890 (pt) cc_final: 0.4582 (pt) REVERT: I 406 GLU cc_start: 0.7239 (pm20) cc_final: 0.6773 (pp20) outliers start: 84 outliers final: 40 residues processed: 691 average time/residue: 0.3870 time to fit residues: 440.6584 Evaluate side-chains 645 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 597 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 393 optimal weight: 9.9990 chunk 324 optimal weight: 1.9990 chunk 360 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 291 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN A1111 ASN C 73 ASN C 171 ASN C 175 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 988 ASN C1041 ASN C1111 ASN C1135 GLN C1201 ASN B 152 GLN B 998 ASN B1001 GLN B1091 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 32025 Z= 0.623 Angle : 0.717 13.172 43707 Z= 0.377 Chirality : 0.053 0.316 5036 Planarity : 0.005 0.080 5600 Dihedral : 5.762 59.783 4900 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 4.02 % Allowed : 10.66 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.65 (0.13), residues: 4001 helix: 0.38 (0.20), residues: 758 sheet: -0.15 (0.18), residues: 842 loop : -2.05 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 332 HIS 0.015 0.002 HIS A 201 PHE 0.036 0.003 PHE C 767 TYR 0.041 0.003 TYR A 49 ARG 0.007 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 636 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6525 (tm-30) REVERT: A 160 HIS cc_start: 0.7673 (p90) cc_final: 0.7274 (p90) REVERT: A 289 GLU cc_start: 0.7259 (tp30) cc_final: 0.7008 (tp30) REVERT: A 400 ASP cc_start: 0.7826 (t0) cc_final: 0.7438 (t0) REVERT: A 463 SER cc_start: 0.8322 (m) cc_final: 0.7946 (t) REVERT: A 464 ASP cc_start: 0.7625 (t0) cc_final: 0.7396 (t70) REVERT: A 500 LYS cc_start: 0.8077 (pptt) cc_final: 0.7506 (pptt) REVERT: A 537 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8144 (mtpp) REVERT: A 733 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8358 (p) REVERT: A 863 GLN cc_start: 0.8068 (tt0) cc_final: 0.7860 (tt0) REVERT: A 977 VAL cc_start: 0.7777 (t) cc_final: 0.7574 (t) REVERT: A 1002 LYS cc_start: 0.7839 (mmmm) cc_final: 0.7571 (mmmm) REVERT: A 1010 LYS cc_start: 0.8301 (ttmm) cc_final: 0.8075 (ttmm) REVERT: A 1013 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 1095 ASP cc_start: 0.7484 (t0) cc_final: 0.7259 (t0) REVERT: C 41 ASP cc_start: 0.7323 (t0) cc_final: 0.7110 (t0) REVERT: C 77 LEU cc_start: 0.8858 (mm) cc_final: 0.8638 (mp) REVERT: C 91 LYS cc_start: 0.8295 (mttp) cc_final: 0.8003 (mttp) REVERT: C 238 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8323 (mtm) REVERT: C 309 PHE cc_start: -0.0968 (OUTLIER) cc_final: -0.1824 (p90) REVERT: C 500 LYS cc_start: 0.8228 (tttm) cc_final: 0.8014 (ptmm) REVERT: C 636 VAL cc_start: 0.8559 (t) cc_final: 0.8356 (p) REVERT: C 845 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: C 883 ASP cc_start: 0.7922 (t70) cc_final: 0.7697 (t0) REVERT: C 885 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8184 (ttpp) REVERT: C 1031 SER cc_start: 0.8266 (m) cc_final: 0.7900 (p) REVERT: C 1069 GLU cc_start: 0.7532 (tp30) cc_final: 0.7126 (tp30) REVERT: C 1071 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7582 (mp10) REVERT: C 1075 ASP cc_start: 0.7329 (t0) cc_final: 0.6826 (t0) REVERT: B 153 TYR cc_start: 0.8437 (m-10) cc_final: 0.8209 (m-10) REVERT: B 155 MET cc_start: 0.6212 (mmm) cc_final: 0.5918 (mmm) REVERT: B 334 ASN cc_start: 0.7875 (t0) cc_final: 0.7445 (t0) REVERT: B 623 ASP cc_start: 0.8025 (t0) cc_final: 0.7782 (t0) REVERT: B 642 ASN cc_start: 0.8412 (m-40) cc_final: 0.8209 (m-40) REVERT: B 666 THR cc_start: 0.8314 (p) cc_final: 0.8019 (p) REVERT: B 821 ASN cc_start: 0.7698 (t0) cc_final: 0.7191 (t0) REVERT: B 934 LEU cc_start: 0.8564 (tp) cc_final: 0.8364 (tp) REVERT: B 1028 LYS cc_start: 0.8368 (mttt) cc_final: 0.8037 (mtpp) REVERT: B 1060 GLU cc_start: 0.7431 (tt0) cc_final: 0.7204 (tt0) REVERT: B 1066 ASP cc_start: 0.7439 (p0) cc_final: 0.6784 (p0) REVERT: B 1069 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: B 1131 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 1167 ASP cc_start: 0.6521 (t70) cc_final: 0.6069 (t70) REVERT: B 1170 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8298 (pt) REVERT: B 1200 LYS cc_start: 0.8314 (ptpp) cc_final: 0.8095 (ptpp) REVERT: T 405 ILE cc_start: 0.4810 (pt) cc_final: 0.4462 (pt) REVERT: T 424 MET cc_start: 0.0756 (OUTLIER) cc_final: 0.0313 (tmm) REVERT: I 406 GLU cc_start: 0.7339 (pm20) cc_final: 0.7085 (pp20) outliers start: 138 outliers final: 80 residues processed: 715 average time/residue: 0.3889 time to fit residues: 456.4715 Evaluate side-chains 690 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 600 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 50.0000 chunk 273 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 365 optimal weight: 20.0000 chunk 386 optimal weight: 20.0000 chunk 190 optimal weight: 0.6980 chunk 346 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS A 595 ASN A 598 ASN C 160 HIS C 171 ASN C 234 HIS ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 954 GLN C1016 GLN C1041 ASN C1180 GLN B 234 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 32025 Z= 0.218 Angle : 0.552 11.340 43707 Z= 0.290 Chirality : 0.045 0.257 5036 Planarity : 0.004 0.080 5600 Dihedral : 5.104 58.452 4898 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.35 % Allowed : 12.90 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.31 (0.13), residues: 4001 helix: 0.97 (0.20), residues: 753 sheet: -0.02 (0.18), residues: 813 loop : -1.88 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 444 HIS 0.007 0.001 HIS A 201 PHE 0.033 0.001 PHE C 661 TYR 0.030 0.002 TYR C 712 ARG 0.005 0.000 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 607 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: A 160 HIS cc_start: 0.7549 (p90) cc_final: 0.7184 (p90) REVERT: A 283 SER cc_start: 0.8284 (t) cc_final: 0.8026 (p) REVERT: A 289 GLU cc_start: 0.7210 (tp30) cc_final: 0.6978 (tp30) REVERT: A 359 LEU cc_start: 0.8543 (tp) cc_final: 0.8271 (tp) REVERT: A 365 VAL cc_start: 0.8979 (p) cc_final: 0.8753 (m) REVERT: A 400 ASP cc_start: 0.7689 (t0) cc_final: 0.7379 (t0) REVERT: A 403 LEU cc_start: 0.9024 (mm) cc_final: 0.8817 (mp) REVERT: A 443 SER cc_start: 0.8250 (t) cc_final: 0.8022 (m) REVERT: A 463 SER cc_start: 0.8350 (m) cc_final: 0.8002 (t) REVERT: A 500 LYS cc_start: 0.7991 (pptt) cc_final: 0.7398 (pptt) REVERT: A 598 ASN cc_start: 0.7713 (m-40) cc_final: 0.7504 (m110) REVERT: A 646 ASN cc_start: 0.7527 (p0) cc_final: 0.7189 (p0) REVERT: A 813 ASP cc_start: 0.7665 (p0) cc_final: 0.7129 (p0) REVERT: A 837 ASP cc_start: 0.6958 (t0) cc_final: 0.6649 (t0) REVERT: A 972 SER cc_start: 0.8743 (p) cc_final: 0.8516 (t) REVERT: A 1010 LYS cc_start: 0.8248 (ttmm) cc_final: 0.8039 (ttmm) REVERT: A 1095 ASP cc_start: 0.7443 (t0) cc_final: 0.7236 (t0) REVERT: A 1112 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 1185 MET cc_start: 0.8183 (mtp) cc_final: 0.7945 (mtp) REVERT: C 91 LYS cc_start: 0.8268 (mttp) cc_final: 0.8027 (mttp) REVERT: C 111 LEU cc_start: 0.7466 (mm) cc_final: 0.7185 (mp) REVERT: C 255 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6827 (mm-30) REVERT: C 309 PHE cc_start: -0.0962 (OUTLIER) cc_final: -0.1824 (p90) REVERT: C 831 GLU cc_start: 0.7502 (pt0) cc_final: 0.7293 (pt0) REVERT: C 845 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: C 851 ASP cc_start: 0.7088 (m-30) cc_final: 0.6836 (m-30) REVERT: C 879 VAL cc_start: 0.8287 (p) cc_final: 0.7997 (m) REVERT: C 912 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7734 (ttmt) REVERT: C 1031 SER cc_start: 0.8213 (m) cc_final: 0.7858 (p) REVERT: C 1069 GLU cc_start: 0.7456 (tp30) cc_final: 0.7014 (tp30) REVERT: C 1075 ASP cc_start: 0.7037 (t0) cc_final: 0.6576 (t0) REVERT: B 155 MET cc_start: 0.6311 (mmm) cc_final: 0.5980 (mmm) REVERT: B 240 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5913 (tt) REVERT: B 320 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7673 (ttm-80) REVERT: B 334 ASN cc_start: 0.7698 (t0) cc_final: 0.7278 (t0) REVERT: B 623 ASP cc_start: 0.7968 (t0) cc_final: 0.7726 (t0) REVERT: B 733 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 744 ILE cc_start: 0.7494 (mm) cc_final: 0.7257 (mm) REVERT: B 821 ASN cc_start: 0.7843 (t0) cc_final: 0.7402 (t0) REVERT: B 933 ASP cc_start: 0.7052 (t0) cc_final: 0.6826 (t0) REVERT: B 1060 GLU cc_start: 0.7324 (tt0) cc_final: 0.7105 (tt0) REVERT: B 1066 ASP cc_start: 0.7311 (p0) cc_final: 0.6408 (p0) REVERT: B 1069 GLU cc_start: 0.7258 (O------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 287 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 329 optimal weight: 0.3980 chunk 267 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.5980 chunk 347 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 924 ASN C 73 ASN C 160 HIS C 171 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C1016 GLN C1041 ASN C1180 GLN B 646 ASN B 856 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32025 Z= 0.272 Angle : 0.558 11.715 43707 Z= 0.292 Chirality : 0.046 0.258 5036 Planarity : 0.004 0.077 5600 Dihedral : 4.957 57.184 4898 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.49 % Allowed : 13.60 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.16 (0.13), residues: 4001 helix: 1.20 (0.20), residues: 753 sheet: 0.02 (0.18), residues: 798 loop : -1.79 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 444 HIS 0.010 0.001 HIS C 201 PHE 0.024 0.002 PHE C 24 TYR 0.028 0.002 TYR B 622 ARG 0.005 0.000 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 604 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: A 160 HIS cc_start: 0.7549 (p90) cc_final: 0.7186 (p90) REVERT: A 283 SER cc_start: 0.8335 (t) cc_final: 0.8056 (p) REVERT: A 289 GLU cc_start: 0.7224 (tp30) cc_final: 0.6978 (tp30) REVERT: A 329 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6702 (tt) REVERT: A 365 VAL cc_start: 0.8977 (p) cc_final: 0.8744 (m) REVERT: A 403 LEU cc_start: 0.9035 (mm) cc_final: 0.8829 (mp) REVERT: A 443 SER cc_start: 0.8291 (t) cc_final: 0.8072 (m) REVERT: A 500 LYS cc_start: 0.7918 (pptt) cc_final: 0.7317 (pptt) REVERT: A 501 TYR cc_start: 0.8008 (m-80) cc_final: 0.7532 (m-80) REVERT: A 556 CYS cc_start: 0.4750 (p) cc_final: 0.4507 (p) REVERT: A 635 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 646 ASN cc_start: 0.7449 (p0) cc_final: 0.7101 (p0) REVERT: A 813 ASP cc_start: 0.7618 (p0) cc_final: 0.7043 (p0) REVERT: A 837 ASP cc_start: 0.6905 (t0) cc_final: 0.6587 (t0) REVERT: A 972 SER cc_start: 0.8715 (p) cc_final: 0.8499 (t) REVERT: A 1010 LYS cc_start: 0.8267 (ttmm) cc_final: 0.8059 (ttmm) REVERT: A 1013 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 1095 ASP cc_start: 0.7409 (t0) cc_final: 0.7208 (t0) REVERT: A 1112 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 1185 MET cc_start: 0.8185 (mtp) cc_final: 0.7946 (mtp) REVERT: C 91 LYS cc_start: 0.8285 (mttp) cc_final: 0.8035 (mttp) REVERT: C 111 LEU cc_start: 0.7443 (mm) cc_final: 0.7163 (mp) REVERT: C 309 PHE cc_start: -0.0945 (OUTLIER) cc_final: -0.1853 (p90) REVERT: C 711 PHE cc_start: 0.7601 (m-10) cc_final: 0.7395 (m-10) REVERT: C 845 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: C 851 ASP cc_start: 0.7107 (m-30) cc_final: 0.6883 (m-30) REVERT: C 879 VAL cc_start: 0.8296 (p) cc_final: 0.8026 (m) REVERT: C 912 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7743 (ttmt) REVERT: C 1031 SER cc_start: 0.8200 (m) cc_final: 0.7857 (p) REVERT: C 1069 GLU cc_start: 0.7457 (tp30) cc_final: 0.6958 (tp30) REVERT: C 1075 ASP cc_start: 0.7068 (t0) cc_final: 0.6572 (t0) REVERT: B 44 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8781 (mt) REVERT: B 155 MET cc_start: 0.6327 (mmm) cc_final: 0.5976 (mmm) REVERT: B 240 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5909 (tt) REVERT: B 320 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7668 (ttm-80) REVERT: B 334 ASN cc_start: 0.7737 (t0) cc_final: 0.7312 (t0) REVERT: B 623 ASP cc_start: 0.8028 (t0) cc_final: 0.7757 (t0) REVERT: B 744 ILE cc_start: 0.7466 (mm) cc_final: 0.7234 (mm) REVERT: B 821 ASN cc_start: 0.7871 (t0) cc_final: 0.7413 (t0) REVERT: B 933 ASP cc_start: 0.7147 (t0) cc_final: 0.6874 (t0) REVERT: B 1060 GLU cc_start: 0.7356 (tt0) cc_final: 0.7147 (tt0) REVERT: B 1069 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: B 1076 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7478 (mtt180) REVERT: B 1131 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 1167 ASP cc_start: 0.6594 (t70) cc_final: 0.6125 (t70) REVERT: T 405 ILE cc_start: 0.4951 (pt) cc_final: 0.4603 (pt) REVERT: T 424 MET cc_start: 0.0858 (OUTLIER) cc_final: 0.0196 (tmm) outliers start: 120 outliers final: 80 residues processed: 678 average time/residue: 0.3947 time to fit residues: 439.0060 Evaluate side-chains 684 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 593 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.9980 chunk 348 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 387 optimal weight: 0.0270 chunk 321 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 32 optimal weight: 0.0670 chunk 128 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 598 ASN C 73 ASN C 140 GLN C 171 ASN C 654 ASN C 954 GLN C1016 GLN C1180 GLN B 642 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 32025 Z= 0.150 Angle : 0.516 14.433 43707 Z= 0.268 Chirality : 0.044 0.258 5036 Planarity : 0.004 0.078 5600 Dihedral : 4.697 55.733 4896 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.71 % Allowed : 14.61 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.97 (0.13), residues: 4001 helix: 1.48 (0.21), residues: 754 sheet: 0.11 (0.18), residues: 797 loop : -1.69 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 444 HIS 0.005 0.001 HIS C 201 PHE 0.046 0.001 PHE C 661 TYR 0.029 0.001 TYR B 712 ARG 0.007 0.000 ARG B1105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 586 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8754 (m-80) cc_final: 0.8369 (m-80) REVERT: A 147 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: A 160 HIS cc_start: 0.7570 (p90) cc_final: 0.7196 (p90) REVERT: A 289 GLU cc_start: 0.7198 (tp30) cc_final: 0.6973 (tp30) REVERT: A 365 VAL cc_start: 0.8934 (p) cc_final: 0.8727 (m) REVERT: A 463 SER cc_start: 0.8380 (m) cc_final: 0.8038 (t) REVERT: A 500 LYS cc_start: 0.7857 (pptt) cc_final: 0.7260 (pptt) REVERT: A 501 TYR cc_start: 0.7921 (m-80) cc_final: 0.7413 (m-80) REVERT: A 635 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 646 ASN cc_start: 0.7408 (p0) cc_final: 0.7071 (p0) REVERT: A 813 ASP cc_start: 0.7495 (p0) cc_final: 0.7003 (p0) REVERT: A 1010 LYS cc_start: 0.8259 (ttmm) cc_final: 0.8046 (ttmm) REVERT: A 1095 ASP cc_start: 0.7404 (t0) cc_final: 0.7203 (t0) REVERT: A 1112 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 1173 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7709 (ttmm) REVERT: A 1185 MET cc_start: 0.8180 (mtp) cc_final: 0.7912 (mtp) REVERT: C 41 ASP cc_start: 0.7258 (t0) cc_final: 0.7055 (t0) REVERT: C 111 LEU cc_start: 0.7416 (mm) cc_final: 0.7155 (mp) REVERT: C 309 PHE cc_start: -0.1015 (OUTLIER) cc_final: -0.1908 (p90) REVERT: C 845 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: C 879 VAL cc_start: 0.8276 (p) cc_final: 0.8002 (m) REVERT: C 912 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7723 (ttmt) REVERT: C 1031 SER cc_start: 0.8163 (m) cc_final: 0.7873 (p) REVERT: C 1069 GLU cc_start: 0.7407 (tp30) cc_final: 0.7016 (tp30) REVERT: B 44 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8763 (mt) REVERT: B 155 MET cc_start: 0.6391 (mmm) cc_final: 0.6036 (mmm) REVERT: B 240 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5902 (tt) REVERT: B 320 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7657 (ttm-80) REVERT: B 334 ASN cc_start: 0.7672 (t0) cc_final: 0.7267 (t0) REVERT: B 660 ASP cc_start: 0.7990 (t0) cc_final: 0.7681 (t70) REVERT: B 714 ASP cc_start: 0.7502 (m-30) cc_final: 0.7186 (m-30) REVERT: B 744 ILE cc_start: 0.7437 (mm) cc_final: 0.7229 (mm) REVERT: B 821 ASN cc_start: 0.7872 (t0) cc_final: 0.7431 (t0) REVERT: B 933 ASP cc_start: 0.7114 (t0) cc_final: 0.6826 (t0) REVERT: B 1060 GLU cc_start: 0.7308 (tt0) cc_final: 0.7102 (tt0) REVERT: B 1069 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: B 1076 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7225 (mtt180) REVERT: B 1131 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 1167 ASP cc_start: 0.6531 (t70) cc_final: 0.6054 (t0) REVERT: T 424 MET cc_start: 0.0775 (OUTLIER) cc_final: 0.0082 (tmm) outliers start: 93 outliers final: 63 residues processed: 642 average time/residue: 0.3913 time to fit residues: 411.2018 Evaluate side-chains 643 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 571 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 50.0000 chunk 43 optimal weight: 0.0970 chunk 220 optimal weight: 0.3980 chunk 282 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 325 optimal weight: 0.9980 chunk 216 optimal weight: 0.4980 chunk 385 optimal weight: 50.0000 chunk 241 optimal weight: 0.0270 chunk 235 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 598 ASN A 799 HIS A 988 ASN C 171 ASN C1016 GLN C1180 GLN B1045 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 32025 Z= 0.156 Angle : 0.512 18.184 43707 Z= 0.264 Chirality : 0.044 0.285 5036 Planarity : 0.004 0.078 5600 Dihedral : 4.532 53.333 4894 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.09 % Allowed : 14.61 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.87 (0.13), residues: 4001 helix: 1.60 (0.21), residues: 759 sheet: 0.10 (0.19), residues: 766 loop : -1.60 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 444 HIS 0.008 0.001 HIS C 201 PHE 0.039 0.001 PHE C 661 TYR 0.027 0.001 TYR C 712 ARG 0.007 0.000 ARG B1105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 579 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8764 (m-80) cc_final: 0.8368 (m-80) REVERT: A 147 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: A 160 HIS cc_start: 0.7548 (p90) cc_final: 0.7179 (p90) REVERT: A 289 GLU cc_start: 0.7212 (tp30) cc_final: 0.6991 (tp30) REVERT: A 329 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6694 (tt) REVERT: A 365 VAL cc_start: 0.8927 (p) cc_final: 0.8721 (m) REVERT: A 463 SER cc_start: 0.8375 (m) cc_final: 0.8036 (t) REVERT: A 500 LYS cc_start: 0.7862 (pptt) cc_final: 0.7271 (pptt) REVERT: A 501 TYR cc_start: 0.7928 (m-80) cc_final: 0.7382 (m-80) REVERT: A 598 ASN cc_start: 0.7705 (m-40) cc_final: 0.7481 (m110) REVERT: A 635 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 646 ASN cc_start: 0.7413 (p0) cc_final: 0.7107 (p0) REVERT: A 813 ASP cc_start: 0.7409 (p0) cc_final: 0.6811 (p0) REVERT: A 884 PHE cc_start: 0.7615 (m-10) cc_final: 0.7288 (m-10) REVERT: A 1010 LYS cc_start: 0.8249 (ttmm) cc_final: 0.8038 (ttmm) REVERT: A 1096 ILE cc_start: 0.8530 (tt) cc_final: 0.8296 (tt) REVERT: A 1112 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 1173 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7704 (ttmm) REVERT: A 1185 MET cc_start: 0.8176 (mtp) cc_final: 0.7927 (mtp) REVERT: C 41 ASP cc_start: 0.7255 (t0) cc_final: 0.7049 (t0) REVERT: C 111 LEU cc_start: 0.7376 (mm) cc_final: 0.7150 (mp) REVERT: C 309 PHE cc_start: -0.1003 (OUTLIER) cc_final: -0.1898 (p90) REVERT: C 845 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: C 879 VAL cc_start: 0.8263 (p) cc_final: 0.7990 (m) REVERT: C 912 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7725 (ttmt) REVERT: C 1031 SER cc_start: 0.8158 (m) cc_final: 0.7868 (p) REVERT: C 1069 GLU cc_start: 0.7383 (tp30) cc_final: 0.7020 (tp30) REVERT: B 44 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8749 (mt) REVERT: B 149 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7133 (p) REVERT: B 155 MET cc_start: 0.6414 (mmm) cc_final: 0.6045 (mmm) REVERT: B 240 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5911 (tt) REVERT: B 320 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7644 (ttm-80) REVERT: B 334 ASN cc_start: 0.7664 (t0) cc_final: 0.7249 (t0) REVERT: B 658 PHE cc_start: 0.8404 (p90) cc_final: 0.8188 (p90) REVERT: B 660 ASP cc_start: 0.7961 (t0) cc_final: 0.7613 (t70) REVERT: B 714 ASP cc_start: 0.7524 (m-30) cc_final: 0.7191 (m-30) REVERT: B 744 ILE cc_start: 0.7417 (mm) cc_final: 0.7214 (mm) REVERT: B 821 ASN cc_start: 0.7853 (t0) cc_final: 0.7432 (t0) REVERT: B 933 ASP cc_start: 0.7143 (t0) cc_final: 0.6835 (t0) REVERT: B 1028 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7943 (mtpp) REVERT: B 1060 GLU cc_start: 0.7320 (tt0) cc_final: 0.7117 (tt0) REVERT: B 1069 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: B 1076 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7188 (mtt90) REVERT: B 1167 ASP cc_start: 0.6514 (t70) cc_final: 0.6039 (t0) REVERT: T 424 MET cc_start: 0.0783 (OUTLIER) cc_final: 0.0003 (tmm) outliers start: 106 outliers final: 71 residues processed: 641 average time/residue: 0.4014 time to fit residues: 423.8359 Evaluate side-chains 652 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 571 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 0.4980 chunk 153 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 245 optimal weight: 0.7980 chunk 262 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN C 171 ASN C 854 GLN C 954 GLN C1180 GLN C1201 ASN B 114 ASN B 646 ASN B1045 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32025 Z= 0.200 Angle : 0.529 15.705 43707 Z= 0.272 Chirality : 0.044 0.252 5036 Planarity : 0.004 0.079 5600 Dihedral : 4.545 54.451 4894 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.94 % Allowed : 14.76 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.84 (0.13), residues: 4001 helix: 1.64 (0.20), residues: 760 sheet: 0.13 (0.19), residues: 752 loop : -1.58 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 444 HIS 0.009 0.001 HIS C 201 PHE 0.041 0.001 PHE C 661 TYR 0.027 0.001 TYR C 712 ARG 0.008 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 576 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8766 (m-80) cc_final: 0.8415 (m-80) REVERT: A 160 HIS cc_start: 0.7548 (p90) cc_final: 0.7169 (p90) REVERT: A 289 GLU cc_start: 0.7225 (tp30) cc_final: 0.6987 (tp30) REVERT: A 365 VAL cc_start: 0.8925 (p) cc_final: 0.8717 (m) REVERT: A 411 SER cc_start: 0.8502 (t) cc_final: 0.8136 (p) REVERT: A 500 LYS cc_start: 0.7850 (pptt) cc_final: 0.7274 (pptt) REVERT: A 501 TYR cc_start: 0.7948 (m-80) cc_final: 0.7729 (m-80) REVERT: A 555 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7743 (ttmm) REVERT: A 635 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 646 ASN cc_start: 0.7448 (p0) cc_final: 0.7140 (p0) REVERT: A 813 ASP cc_start: 0.7468 (p0) cc_final: 0.6897 (p0) REVERT: A 884 PHE cc_start: 0.7633 (m-10) cc_final: 0.7331 (m-10) REVERT: A 981 LEU cc_start: 0.8264 (mt) cc_final: 0.8049 (mp) REVERT: A 1013 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 1096 ILE cc_start: 0.8533 (tt) cc_final: 0.8284 (tt) REVERT: A 1112 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 1173 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7703 (ttmm) REVERT: A 1185 MET cc_start: 0.8179 (mtp) cc_final: 0.7953 (mtp) REVERT: C 111 LEU cc_start: 0.7376 (mm) cc_final: 0.7150 (mp) REVERT: C 309 PHE cc_start: -0.0992 (OUTLIER) cc_final: -0.1886 (p90) REVERT: C 845 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: C 879 VAL cc_start: 0.8276 (p) cc_final: 0.8002 (m) REVERT: C 912 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7729 (ttmt) REVERT: C 1031 SER cc_start: 0.8184 (m) cc_final: 0.7892 (p) REVERT: C 1069 GLU cc_start: 0.7381 (tp30) cc_final: 0.7007 (tp30) REVERT: B 44 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8772 (mt) REVERT: B 155 MET cc_start: 0.6415 (mmm) cc_final: 0.6107 (mmm) REVERT: B 240 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5889 (tt) REVERT: B 320 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7655 (ttm-80) REVERT: B 334 ASN cc_start: 0.7673 (t0) cc_final: 0.7275 (t0) REVERT: B 714 ASP cc_start: 0.7534 (m-30) cc_final: 0.7149 (m-30) REVERT: B 821 ASN cc_start: 0.7890 (t0) cc_final: 0.7456 (t0) REVERT: B 933 ASP cc_start: 0.7176 (t0) cc_final: 0.6872 (t0) REVERT: B 1060 GLU cc_start: 0.7344 (tt0) cc_final: 0.7141 (tt0) REVERT: B 1069 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: B 1076 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7263 (mtt180) REVERT: B 1167 ASP cc_start: 0.6538 (t70) cc_final: 0.6062 (t0) REVERT: T 424 MET cc_start: 0.0764 (OUTLIER) cc_final: -0.0028 (tmm) outliers start: 101 outliers final: 82 residues processed: 634 average time/residue: 0.3813 time to fit residues: 395.7463 Evaluate side-chains 657 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 567 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 216 optimal weight: 0.7980 chunk 156 optimal weight: 0.0170 chunk 282 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 324 optimal weight: 0.6980 chunk 339 optimal weight: 1.9990 chunk 358 optimal weight: 0.7980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN C 171 ASN C 854 GLN C 954 GLN ** C 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 GLN C1201 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32025 Z= 0.212 Angle : 0.550 23.596 43707 Z= 0.280 Chirality : 0.044 0.277 5036 Planarity : 0.004 0.080 5600 Dihedral : 4.589 54.693 4894 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.94 % Allowed : 14.91 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.83 (0.13), residues: 4001 helix: 1.63 (0.20), residues: 761 sheet: 0.11 (0.18), residues: 772 loop : -1.57 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 444 HIS 0.009 0.001 HIS C 201 PHE 0.039 0.001 PHE C 661 TYR 0.031 0.001 TYR B 712 ARG 0.008 0.000 ARG B1105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 565 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8772 (m-80) cc_final: 0.8370 (m-80) REVERT: A 160 HIS cc_start: 0.7529 (p90) cc_final: 0.7107 (p90) REVERT: A 289 GLU cc_start: 0.7223 (tp30) cc_final: 0.6986 (tp30) REVERT: A 365 VAL cc_start: 0.8924 (p) cc_final: 0.8717 (m) REVERT: A 411 SER cc_start: 0.8509 (t) cc_final: 0.8140 (p) REVERT: A 500 LYS cc_start: 0.7844 (pptt) cc_final: 0.7280 (pptt) REVERT: A 555 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7775 (ttmm) REVERT: A 635 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 813 ASP cc_start: 0.7484 (p0) cc_final: 0.7008 (p0) REVERT: A 884 PHE cc_start: 0.7662 (m-10) cc_final: 0.7356 (m-10) REVERT: A 981 LEU cc_start: 0.8255 (mt) cc_final: 0.8027 (mp) REVERT: A 1013 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 1096 ILE cc_start: 0.8526 (tt) cc_final: 0.8286 (tt) REVERT: A 1112 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 1173 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7701 (ttmm) REVERT: A 1185 MET cc_start: 0.8184 (mtp) cc_final: 0.7952 (mtp) REVERT: C 111 LEU cc_start: 0.7386 (mm) cc_final: 0.7162 (mp) REVERT: C 309 PHE cc_start: -0.0960 (OUTLIER) cc_final: -0.1875 (p90) REVERT: C 845 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: C 879 VAL cc_start: 0.8288 (p) cc_final: 0.8008 (m) REVERT: C 912 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7724 (ttmt) REVERT: C 1031 SER cc_start: 0.8195 (m) cc_final: 0.7888 (p) REVERT: C 1069 GLU cc_start: 0.7366 (tp30) cc_final: 0.6888 (tp30) REVERT: B 44 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 149 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7221 (p) REVERT: B 155 MET cc_start: 0.6466 (mmm) cc_final: 0.6142 (mmm) REVERT: B 240 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5889 (tt) REVERT: B 320 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7674 (ttm-80) REVERT: B 334 ASN cc_start: 0.7674 (t0) cc_final: 0.7280 (t0) REVERT: B 821 ASN cc_start: 0.7878 (t0) cc_final: 0.7428 (t0) REVERT: B 933 ASP cc_start: 0.7201 (t0) cc_final: 0.6902 (t0) REVERT: B 1060 GLU cc_start: 0.7353 (tt0) cc_final: 0.7140 (tt0) REVERT: B 1066 ASP cc_start: 0.7251 (p0) cc_final: 0.6323 (p0) REVERT: B 1069 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: B 1076 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: B 1167 ASP cc_start: 0.6577 (t70) cc_final: 0.6103 (t0) REVERT: T 424 MET cc_start: 0.0784 (OUTLIER) cc_final: -0.0073 (tmm) outliers start: 101 outliers final: 83 residues processed: 624 average time/residue: 0.3974 time to fit residues: 407.6078 Evaluate side-chains 655 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 563 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 10.0000 chunk 379 optimal weight: 50.0000 chunk 231 optimal weight: 0.7980 chunk 180 optimal weight: 0.0070 chunk 264 optimal weight: 4.9990 chunk 398 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 245 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 646 ASN C 854 GLN C 954 GLN C 998 ASN C1180 GLN C1201 ASN B 646 ASN B1045 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32025 Z= 0.173 Angle : 0.538 21.058 43707 Z= 0.275 Chirality : 0.044 0.249 5036 Planarity : 0.004 0.080 5600 Dihedral : 4.544 54.468 4894 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.65 % Allowed : 15.37 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4001 helix: 1.64 (0.20), residues: 767 sheet: 0.13 (0.19), residues: 762 loop : -1.54 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 444 HIS 0.008 0.001 HIS C 201 PHE 0.038 0.001 PHE C 661 TYR 0.028 0.001 TYR B 712 ARG 0.008 0.000 ARG A 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 564 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8779 (m-80) cc_final: 0.8390 (m-80) REVERT: A 160 HIS cc_start: 0.7506 (p90) cc_final: 0.7094 (p90) REVERT: A 289 GLU cc_start: 0.7219 (tp30) cc_final: 0.6980 (tp30) REVERT: A 365 VAL cc_start: 0.8910 (p) cc_final: 0.8704 (m) REVERT: A 411 SER cc_start: 0.8506 (t) cc_final: 0.8134 (p) REVERT: A 500 LYS cc_start: 0.7844 (pptt) cc_final: 0.7264 (pptt) REVERT: A 555 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7780 (ttmm) REVERT: A 598 ASN cc_start: 0.7674 (m-40) cc_final: 0.7469 (m110) REVERT: A 635 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 813 ASP cc_start: 0.7435 (p0) cc_final: 0.6977 (p0) REVERT: A 884 PHE cc_start: 0.7603 (m-10) cc_final: 0.7288 (m-10) REVERT: A 981 LEU cc_start: 0.8250 (mt) cc_final: 0.7997 (mp) REVERT: A 1096 ILE cc_start: 0.8538 (tt) cc_final: 0.8290 (tt) REVERT: A 1112 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 1173 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7694 (ttmm) REVERT: A 1185 MET cc_start: 0.8181 (mtp) cc_final: 0.7957 (mtp) REVERT: C 111 LEU cc_start: 0.7347 (mm) cc_final: 0.7126 (mp) REVERT: C 309 PHE cc_start: -0.0969 (OUTLIER) cc_final: -0.1891 (p90) REVERT: C 845 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: C 879 VAL cc_start: 0.8292 (p) cc_final: 0.8014 (m) REVERT: C 912 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7718 (ttmt) REVERT: C 1031 SER cc_start: 0.8185 (m) cc_final: 0.7889 (p) REVERT: C 1069 GLU cc_start: 0.7337 (tp30) cc_final: 0.6877 (tp30) REVERT: B 44 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8786 (mt) REVERT: B 149 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7231 (p) REVERT: B 155 MET cc_start: 0.6468 (mmm) cc_final: 0.6139 (mmm) REVERT: B 240 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5891 (tt) REVERT: B 320 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7649 (ttm-80) REVERT: B 334 ASN cc_start: 0.7669 (t0) cc_final: 0.7277 (t0) REVERT: B 821 ASN cc_start: 0.7883 (t0) cc_final: 0.7455 (t0) REVERT: B 933 ASP cc_start: 0.7198 (t0) cc_final: 0.6882 (t0) REVERT: B 1060 GLU cc_start: 0.7339 (tt0) cc_final: 0.7128 (tt0) REVERT: B 1066 ASP cc_start: 0.7226 (p0) cc_final: 0.6257 (p0) REVERT: B 1069 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: B 1076 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7215 (mtt180) REVERT: B 1167 ASP cc_start: 0.6577 (t70) cc_final: 0.6102 (t0) REVERT: T 424 MET cc_start: 0.0748 (OUTLIER) cc_final: -0.0102 (tmm) outliers start: 91 outliers final: 77 residues processed: 617 average time/residue: 0.3997 time to fit residues: 404.4575 Evaluate side-chains 643 residues out of total 3583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 558 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 1.9990 chunk 338 optimal weight: 0.0030 chunk 97 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN C 854 GLN C 954 GLN C1180 GLN C1201 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.170373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126475 restraints weight = 48976.572| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.60 r_work: 0.3369 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 32025 Z= 0.212 Angle : 0.665 59.199 43707 Z= 0.370 Chirality : 0.047 1.025 5036 Planarity : 0.004 0.127 5600 Dihedral : 4.542 54.504 4894 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.59 % Allowed : 15.37 % Favored : 82.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4001 helix: 1.64 (0.20), residues: 767 sheet: 0.13 (0.19), residues: 762 loop : -1.54 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 444 HIS 0.007 0.001 HIS C 201 PHE 0.035 0.001 PHE C 661 TYR 0.030 0.001 TYR A 458 ARG 0.006 0.000 ARG B1105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9994.38 seconds wall clock time: 266 minutes 59.25 seconds (16019.25 seconds total)