Starting phenix.real_space_refine on Mon Feb 19 02:27:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgh_22870/02_2024/7kgh_22870_updated.pdb" } resolution = 3.79 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 135 5.16 5 C 15234 2.51 5 N 3801 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 724": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B ARG 833": "NH1" <-> "NH2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B GLU 849": "OE1" <-> "OE2" Residue "B GLU 884": "OE1" <-> "OE2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 963": "NH1" <-> "NH2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "C ARG 724": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C ARG 809": "NH1" <-> "NH2" Residue "C ARG 813": "NH1" <-> "NH2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 884": "OE1" <-> "OE2" Residue "C ARG 910": "NH1" <-> "NH2" Residue "C GLU 946": "OE1" <-> "OE2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 963": "NH1" <-> "NH2" Residue "C GLU 1024": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' ET': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 12.34, per 1000 atoms: 0.52 Number of scatterers: 23505 At special positions: 0 Unit cell: (122.04, 113.4, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 3 15.00 O 4332 8.00 N 3801 7.00 C 15234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 9.42 Conformation dependent library (CDL) restraints added in 3.7 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 22 sheets defined 55.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.068A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.750A pdb=" N ASP A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.697A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 114 removed outlier: 3.512A pdb=" N VAL A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 190 through 196 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.762A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 Processing helix chain 'A' and resid 362 through 386 removed outlier: 4.435A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.624A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 423 removed outlier: 3.783A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 removed outlier: 5.391A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.905A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.228A pdb=" N PHE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 496 removed outlier: 3.584A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.857A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 555 Processing helix chain 'A' and resid 581 through 597 Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 684 through 700 removed outlier: 4.083A pdb=" N LEU A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 774 through 779 Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 828 through 841 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 861 through 883 removed outlier: 4.651A pdb=" N ALA A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.643A pdb=" N LEU A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL A 896 " --> pdb=" O VAL A 892 " (cutoff:3.500A) Proline residue: A 897 - end of helix Processing helix chain 'A' and resid 916 through 946 removed outlier: 3.636A pdb=" N THR A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 980 removed outlier: 5.053A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 987 through 1026 removed outlier: 4.340A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 9 through 29 Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.860A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 4.191A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 190 through 196 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 316 removed outlier: 4.070A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 3.805A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 386 Proline residue: B 368 - end of helix removed outlier: 4.306A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 422 removed outlier: 4.188A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 Processing helix chain 'B' and resid 439 through 458 removed outlier: 4.024A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.897A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 495 removed outlier: 3.619A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 555 removed outlier: 3.758A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Proline residue: B 537 - end of helix removed outlier: 3.528A pdb=" N ALA B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 597 removed outlier: 4.308A pdb=" N ASP B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 649 Processing helix chain 'B' and resid 684 through 699 removed outlier: 3.565A pdb=" N LEU B 688 " --> pdb=" O MET B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 734 through 742 removed outlier: 3.585A pdb=" N ILE B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 828 through 841 removed outlier: 3.740A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 883 removed outlier: 4.915A pdb=" N ALA B 865 " --> pdb=" O GLU B 861 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 910 removed outlier: 3.669A pdb=" N VAL B 892 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 895 " --> pdb=" O SER B 891 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 896 " --> pdb=" O VAL B 892 " (cutoff:3.500A) Proline residue: B 897 - end of helix removed outlier: 4.362A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 945 removed outlier: 4.222A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 960 Processing helix chain 'B' and resid 962 through 981 Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 987 through 1006 removed outlier: 4.064A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1026 Proline residue: B1013 - end of helix removed outlier: 3.598A pdb=" N VAL B1023 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 9 through 29 Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 62 through 71 removed outlier: 3.971A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLY C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 116 removed outlier: 4.324A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 115 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.518A pdb=" N LYS C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 168' Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 299 through 316 removed outlier: 3.802A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.727A pdb=" N LEU C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix removed outlier: 3.550A pdb=" N PHE C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 423 removed outlier: 4.409A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 457 removed outlier: 5.453A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.545A pdb=" N LEU C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Proline residue: C 455 - end of helix Processing helix chain 'C' and resid 462 through 496 removed outlier: 3.788A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 509 through 533 Processing helix chain 'C' and resid 535 through 555 removed outlier: 3.748A pdb=" N MET C 539 " --> pdb=" O THR C 535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 541 " --> pdb=" O PRO C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 595 removed outlier: 3.582A pdb=" N LEU C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 Processing helix chain 'C' and resid 684 through 700 removed outlier: 3.663A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 734 through 745 Processing helix chain 'C' and resid 774 through 779 Processing helix chain 'C' and resid 792 through 794 No H-bonds generated for 'chain 'C' and resid 792 through 794' Processing helix chain 'C' and resid 828 through 841 removed outlier: 4.310A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 859 Processing helix chain 'C' and resid 863 through 883 Processing helix chain 'C' and resid 888 through 910 removed outlier: 3.567A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL C 895 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 896 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Proline residue: C 897 - end of helix removed outlier: 4.029A pdb=" N ILE C 900 " --> pdb=" O VAL C 896 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 947 removed outlier: 3.601A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 980 removed outlier: 4.765A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 987 through 1026 removed outlier: 4.208A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C1002 " --> pdb=" O PHE C 998 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix removed outlier: 3.770A pdb=" N GLU C1024 " --> pdb=" O LEU C1020 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.346A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 83 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 287 through 291 Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.569A pdb=" N GLU A 269 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N MET A 759 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N MET A 184 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN A 761 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE A 186 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 763 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 188 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN A 765 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 250 through 252 Processing sheet with id= E, first strand: chain 'A' and resid 278 through 280 removed outlier: 6.772A pdb=" N THR A 625 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE A 623 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA A 606 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 621 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU A 608 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 619 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 847 through 850 removed outlier: 4.610A pdb=" N SER A 817 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 715 through 719 Processing sheet with id= H, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.820A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 322 through 324 removed outlier: 3.565A pdb=" N LEU B 137 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 291 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 139 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 289 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY B 141 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR B 287 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 266 through 272 Processing sheet with id= K, first strand: chain 'B' and resid 250 through 252 Processing sheet with id= L, first strand: chain 'B' and resid 278 through 280 removed outlier: 7.173A pdb=" N THR B 625 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE B 623 " --> pdb=" O ASN B 604 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA B 606 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 621 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU B 608 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL B 619 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 714 through 718 Processing sheet with id= N, first strand: chain 'B' and resid 752 through 755 Processing sheet with id= O, first strand: chain 'B' and resid 704 through 709 removed outlier: 7.134A pdb=" N ILE B 821 " --> pdb=" O TYR B 705 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B 707 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 819 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.861A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 139 through 143 removed outlier: 3.821A pdb=" N THR C 287 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.457A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 217 through 219 Processing sheet with id= T, first strand: chain 'C' and resid 278 through 281 removed outlier: 4.270A pdb=" N SER C 603 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 846 through 850 removed outlier: 4.116A pdb=" N SER C 817 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 715 through 722 1326 hydrogen bonds defined for protein. 3885 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: 8.85 Time building geometry restraints manager: 10.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 3843 1.26 - 1.40: 5291 1.40 - 1.54: 14153 1.54 - 1.68: 383 1.68 - 1.82: 264 Bond restraints: 23934 Sorted by residual: bond pdb=" C ASN B 205 " pdb=" O ASN B 205 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.17e-02 7.31e+03 8.21e+01 bond pdb=" C HIS C 342 " pdb=" O HIS C 342 " ideal model delta sigma weight residual 1.237 1.132 0.105 1.17e-02 7.31e+03 8.02e+01 bond pdb=" C GLN C 863 " pdb=" O GLN C 863 " ideal model delta sigma weight residual 1.236 1.126 0.110 1.26e-02 6.30e+03 7.68e+01 bond pdb=" C8 PTY B1101 " pdb=" O7 PTY B1101 " ideal model delta sigma weight residual 1.331 1.458 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C ASN C 298 " pdb=" O ASN C 298 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.21e-02 6.83e+03 3.55e+01 ... (remaining 23929 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.57: 572 105.57 - 112.68: 12920 112.68 - 119.80: 7676 119.80 - 126.91: 11057 126.91 - 134.03: 217 Bond angle restraints: 32442 Sorted by residual: angle pdb=" C ASN C 298 " pdb=" N ALA C 299 " pdb=" CA ALA C 299 " ideal model delta sigma weight residual 120.44 130.93 -10.49 1.30e+00 5.92e-01 6.51e+01 angle pdb=" CA ASN C 298 " pdb=" C ASN C 298 " pdb=" O ASN C 298 " ideal model delta sigma weight residual 120.49 112.27 8.22 1.16e+00 7.43e-01 5.02e+01 angle pdb=" CA HIS C 342 " pdb=" C HIS C 342 " pdb=" O HIS C 342 " ideal model delta sigma weight residual 120.55 113.11 7.44 1.06e+00 8.90e-01 4.92e+01 angle pdb=" CA ASN B 205 " pdb=" C ASN B 205 " pdb=" O ASN B 205 " ideal model delta sigma weight residual 120.55 113.41 7.14 1.06e+00 8.90e-01 4.54e+01 angle pdb=" CA PHE C 550 " pdb=" C PHE C 550 " pdb=" O PHE C 550 " ideal model delta sigma weight residual 119.97 112.47 7.50 1.15e+00 7.56e-01 4.25e+01 ... (remaining 32437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 14102 32.59 - 65.19: 351 65.19 - 97.78: 34 97.78 - 130.38: 1 130.38 - 162.97: 1 Dihedral angle restraints: 14489 sinusoidal: 5672 harmonic: 8817 Sorted by residual: dihedral pdb=" C TYR A 77 " pdb=" N TYR A 77 " pdb=" CA TYR A 77 " pdb=" CB TYR A 77 " ideal model delta harmonic sigma weight residual -122.60 -137.51 14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CA TYR A 77 " pdb=" CB TYR A 77 " ideal model delta harmonic sigma weight residual 122.80 136.64 -13.84 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" C ASN A 74 " pdb=" N ASN A 74 " pdb=" CA ASN A 74 " pdb=" CB ASN A 74 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 ... (remaining 14486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3733 0.111 - 0.221: 125 0.221 - 0.332: 13 0.332 - 0.443: 0 0.443 - 0.553: 2 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA TYR A 77 " pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CB TYR A 77 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CA ASN A 74 " pdb=" N ASN A 74 " pdb=" C ASN A 74 " pdb=" CB ASN A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ILE A 291 " pdb=" N ILE A 291 " pdb=" C ILE A 291 " pdb=" CB ILE A 291 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 3870 not shown) Planarity restraints: 4066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 330 " 0.077 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO B 331 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 765 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLN B 765 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN B 765 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL B 766 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 44 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASN A 44 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN A 44 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 45 " -0.025 2.00e-02 2.50e+03 ... (remaining 4063 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 102 2.51 - 3.11: 18682 3.11 - 3.70: 35952 3.70 - 4.30: 51301 4.30 - 4.90: 85663 Nonbonded interactions: 191700 Sorted by model distance: nonbonded pdb=" O ASN B 248 " pdb=" ND2 ASN B 248 " model vdw 1.910 2.520 nonbonded pdb=" OH TYR A 749 " pdb=" OD1 ASP A 752 " model vdw 2.062 2.440 nonbonded pdb=" O LEU B 898 " pdb=" OG SER B1003 " model vdw 2.074 2.440 nonbonded pdb=" OE1 GLN B 120 " pdb=" NH2 ARG B 123 " model vdw 2.093 2.520 nonbonded pdb=" NZ LYS C 602 " pdb=" O LYS C 627 " model vdw 2.095 2.520 ... (remaining 191695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.020 Extract box with map and model: 2.100 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 61.500 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.005 0.127 23934 Z= 0.311 Angle : 0.816 17.008 32442 Z= 0.506 Chirality : 0.047 0.553 3873 Planarity : 0.006 0.114 4066 Dihedral : 14.421 162.970 8783 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.97 % Allowed : 1.33 % Favored : 97.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.17 % 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: 1.37 (0.15), residues: 3048 helix: 1.80 (0.13), residues: 1644 sheet: -0.01 (0.24), residues: 402 loop : -0.08 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 800 HIS 0.003 0.001 HIS C 991 PHE 0.038 0.001 PHE B 136 TYR 0.028 0.002 TYR C 78 ARG 0.018 0.001 ARG C 961 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 569 time to evaluate : 2.531 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 156 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6621 (t70) REVERT: A 280 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6270 (mm) REVERT: A 304 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6586 (tt0) REVERT: A 376 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6291 (mp) REVERT: A 693 GLU cc_start: 0.7370 (tp30) cc_final: 0.6907 (tm-30) REVERT: A 807 TYR cc_start: 0.7869 (m-80) cc_final: 0.7449 (m-80) REVERT: A 1001 MET cc_start: 0.5262 (ttm) cc_final: 0.4998 (ttm) REVERT: B 165 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: B 184 MET cc_start: 0.6706 (mmm) cc_final: 0.6097 (mmm) REVERT: B 309 LYS cc_start: 0.7709 (tptp) cc_final: 0.7283 (tptp) REVERT: B 527 MET cc_start: 0.6965 (ttt) cc_final: 0.6667 (ttm) REVERT: B 654 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5681 (pt0) REVERT: B 695 MET cc_start: 0.7395 (mmm) cc_final: 0.6715 (mmt) REVERT: B 813 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6966 (mtt-85) REVERT: B 844 LYS cc_start: 0.7329 (tppt) cc_final: 0.7085 (tppt) REVERT: B 931 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7341 (tttm) REVERT: C 8 ARG cc_start: 0.7374 (mtt180) cc_final: 0.7032 (mmm-85) REVERT: C 68 GLU cc_start: 0.6175 (mp0) cc_final: 0.5501 (mp0) REVERT: C 363 ARG cc_start: 0.7138 (mmt180) cc_final: 0.6759 (mmt-90) REVERT: C 423 GLU cc_start: 0.7086 (mp0) cc_final: 0.6673 (mp0) REVERT: C 467 TYR cc_start: 0.7398 (m-10) cc_final: 0.7116 (m-80) REVERT: C 471 THR cc_start: 0.7946 (m) cc_final: 0.7712 (p) REVERT: C 533 LYS cc_start: 0.7601 (tmtt) cc_final: 0.7371 (tptp) REVERT: C 589 ASN cc_start: 0.6050 (m110) cc_final: 0.5624 (m-40) REVERT: C 826 THR cc_start: 0.8084 (m) cc_final: 0.7878 (m) outliers start: 25 outliers final: 5 residues processed: 589 average time/residue: 0.3501 time to fit residues: 328.7812 Evaluate side-chains 520 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 508 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 813 ARG Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 0.3980 chunk 128 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 342 HIS A 590 GLN A 701 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN B 360 HIS B 566 GLN B 617 GLN B 801 ASN B 859 GLN B 863 GLN C 282 ASN C 566 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 991 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23934 Z= 0.317 Angle : 0.661 12.735 32442 Z= 0.339 Chirality : 0.045 0.282 3873 Planarity : 0.005 0.060 4066 Dihedral : 7.852 166.521 3308 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.11 % Allowed : 9.86 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.21 (0.15), residues: 3048 helix: 1.65 (0.13), residues: 1651 sheet: -0.05 (0.23), residues: 421 loop : -0.16 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 800 HIS 0.003 0.001 HIS C 534 PHE 0.033 0.002 PHE A 517 TYR 0.022 0.002 TYR C 848 ARG 0.005 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 539 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4485 (tpp) cc_final: 0.4252 (mmt) REVERT: A 68 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6630 (mm-30) REVERT: A 304 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: A 311 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7241 (mm-30) REVERT: A 398 MET cc_start: 0.7774 (mtm) cc_final: 0.7444 (mtp) REVERT: A 474 MET cc_start: 0.6513 (ttt) cc_final: 0.6244 (ttt) REVERT: A 570 MET cc_start: 0.7680 (ttp) cc_final: 0.7336 (ttm) REVERT: A 693 GLU cc_start: 0.7392 (tp30) cc_final: 0.7054 (tp30) REVERT: B 153 ASP cc_start: 0.7228 (m-30) cc_final: 0.6996 (m-30) REVERT: B 165 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6804 (mm-30) REVERT: B 522 LYS cc_start: 0.7486 (mtmm) cc_final: 0.7119 (mtmm) REVERT: B 527 MET cc_start: 0.6925 (ttt) cc_final: 0.6636 (ttm) REVERT: B 554 LYS cc_start: 0.7407 (mptt) cc_final: 0.7129 (tppt) REVERT: B 654 GLU cc_start: 0.6336 (mt-10) cc_final: 0.5909 (pt0) REVERT: B 656 MET cc_start: 0.7505 (tpp) cc_final: 0.7001 (tpt) REVERT: B 714 GLN cc_start: 0.7564 (mt0) cc_final: 0.7360 (mt0) REVERT: B 783 MET cc_start: 0.3676 (mmm) cc_final: 0.3110 (mmm) REVERT: B 844 LYS cc_start: 0.7354 (tppt) cc_final: 0.7137 (tppt) REVERT: C 8 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7323 (mtt180) REVERT: C 68 GLU cc_start: 0.6469 (mp0) cc_final: 0.5481 (mp0) REVERT: C 213 GLU cc_start: 0.7282 (tt0) cc_final: 0.7067 (tt0) REVERT: C 321 MET cc_start: 0.6683 (mtm) cc_final: 0.6369 (mtm) REVERT: C 356 TYR cc_start: 0.6530 (t80) cc_final: 0.6209 (t80) REVERT: C 423 GLU cc_start: 0.7178 (mp0) cc_final: 0.6776 (mp0) REVERT: C 467 TYR cc_start: 0.7426 (m-10) cc_final: 0.7223 (m-80) REVERT: C 528 LEU cc_start: 0.5925 (tp) cc_final: 0.5656 (tp) REVERT: C 589 ASN cc_start: 0.6156 (m110) cc_final: 0.5804 (m-40) REVERT: C 602 LYS cc_start: 0.7744 (mttp) cc_final: 0.7479 (mmtm) REVERT: C 769 LYS cc_start: 0.7866 (tmmt) cc_final: 0.7476 (tmtt) REVERT: C 826 THR cc_start: 0.8138 (m) cc_final: 0.7638 (p) outliers start: 54 outliers final: 30 residues processed: 570 average time/residue: 0.3256 time to fit residues: 294.3057 Evaluate side-chains 535 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 503 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 276 optimal weight: 0.2980 chunk 94 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 765 GLN C 108 GLN C 589 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23934 Z= 0.242 Angle : 0.598 10.402 32442 Z= 0.307 Chirality : 0.043 0.197 3873 Planarity : 0.005 0.055 4066 Dihedral : 7.142 163.179 3292 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.65 % Allowed : 12.28 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.14 (0.15), residues: 3048 helix: 1.57 (0.13), residues: 1662 sheet: -0.11 (0.23), residues: 441 loop : -0.14 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 800 HIS 0.002 0.001 HIS C 534 PHE 0.031 0.001 PHE A 517 TYR 0.024 0.002 TYR C 848 ARG 0.005 0.000 ARG C 771 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 532 time to evaluate : 2.751 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 1 MET cc_start: 0.4725 (tpp) cc_final: 0.4465 (mmt) REVERT: A 68 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6569 (mm-30) REVERT: A 99 ASP cc_start: 0.5149 (OUTLIER) cc_final: 0.4568 (p0) REVERT: A 304 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6600 (tt0) REVERT: A 474 MET cc_start: 0.6550 (ttt) cc_final: 0.6238 (ttt) REVERT: A 570 MET cc_start: 0.7609 (ttp) cc_final: 0.7355 (ttm) REVERT: A 693 GLU cc_start: 0.7357 (tp30) cc_final: 0.7021 (tp30) REVERT: A 769 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6233 (ttpt) REVERT: A 884 GLU cc_start: 0.6749 (mp0) cc_final: 0.6394 (mp0) REVERT: A 939 PHE cc_start: 0.6548 (m-80) cc_final: 0.6133 (t80) REVERT: B 165 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6697 (mm-30) REVERT: B 184 MET cc_start: 0.5855 (mmp) cc_final: 0.5490 (mmm) REVERT: B 518 ASP cc_start: 0.6419 (t0) cc_final: 0.6195 (t0) REVERT: B 522 LYS cc_start: 0.7507 (mtmm) cc_final: 0.7120 (mtmm) REVERT: B 527 MET cc_start: 0.6887 (ttt) cc_final: 0.6585 (ttm) REVERT: B 554 LYS cc_start: 0.7396 (mptt) cc_final: 0.7170 (tppt) REVERT: B 654 GLU cc_start: 0.6391 (mt-10) cc_final: 0.5956 (pt0) REVERT: B 656 MET cc_start: 0.7506 (tpp) cc_final: 0.6704 (tpt) REVERT: B 714 GLN cc_start: 0.7888 (mt0) cc_final: 0.7542 (mt0) REVERT: B 783 MET cc_start: 0.3442 (mmm) cc_final: 0.2952 (mmm) REVERT: C 8 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7361 (mtt180) REVERT: C 68 GLU cc_start: 0.6543 (mp0) cc_final: 0.5626 (mp0) REVERT: C 213 GLU cc_start: 0.7338 (tt0) cc_final: 0.7114 (tt0) REVERT: C 321 MET cc_start: 0.6750 (mtm) cc_final: 0.6506 (mtm) REVERT: C 356 TYR cc_start: 0.6494 (t80) cc_final: 0.6200 (t80) REVERT: C 423 GLU cc_start: 0.7226 (mp0) cc_final: 0.6902 (mp0) REVERT: C 467 TYR cc_start: 0.7421 (m-10) cc_final: 0.7012 (m-80) REVERT: C 498 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7463 (mttp) REVERT: C 589 ASN cc_start: 0.6236 (m-40) cc_final: 0.5861 (m-40) REVERT: C 654 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6228 (tp30) REVERT: C 769 LYS cc_start: 0.7867 (tmmt) cc_final: 0.7463 (tmtt) REVERT: C 826 THR cc_start: 0.8147 (m) cc_final: 0.7658 (p) outliers start: 68 outliers final: 41 residues processed: 560 average time/residue: 0.3540 time to fit residues: 312.7722 Evaluate side-chains 557 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 512 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN B 360 HIS B 604 ASN B 649 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23934 Z= 0.277 Angle : 0.615 12.225 32442 Z= 0.314 Chirality : 0.043 0.295 3873 Planarity : 0.005 0.059 4066 Dihedral : 6.968 154.114 3292 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.96 % Allowed : 14.31 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.07 (0.15), residues: 3048 helix: 1.54 (0.13), residues: 1652 sheet: -0.14 (0.23), residues: 448 loop : -0.20 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 800 HIS 0.002 0.001 HIS C 360 PHE 0.029 0.002 PHE A 517 TYR 0.025 0.002 TYR C 848 ARG 0.005 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 528 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6630 (mm-30) REVERT: A 99 ASP cc_start: 0.5196 (OUTLIER) cc_final: 0.4679 (p0) REVERT: A 213 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6387 (mt-10) REVERT: A 435 MET cc_start: 0.4871 (mmm) cc_final: 0.4656 (mmm) REVERT: A 474 MET cc_start: 0.6385 (ttt) cc_final: 0.6183 (ttt) REVERT: A 684 MET cc_start: 0.7275 (mpp) cc_final: 0.5360 (mmm) REVERT: A 693 GLU cc_start: 0.7383 (tp30) cc_final: 0.7040 (tp30) REVERT: A 706 MET cc_start: 0.6292 (mtp) cc_final: 0.6025 (mtt) REVERT: A 769 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6289 (ttpt) REVERT: A 872 MET cc_start: 0.7159 (mpp) cc_final: 0.6877 (mpp) REVERT: A 884 GLU cc_start: 0.6656 (mp0) cc_final: 0.6321 (mp0) REVERT: A 939 PHE cc_start: 0.6525 (m-80) cc_final: 0.6069 (t80) REVERT: B 165 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: B 184 MET cc_start: 0.5987 (mmp) cc_final: 0.5559 (mmm) REVERT: B 518 ASP cc_start: 0.6480 (t0) cc_final: 0.6251 (t0) REVERT: B 522 LYS cc_start: 0.7548 (mtmm) cc_final: 0.7193 (mtmm) REVERT: B 527 MET cc_start: 0.6936 (ttt) cc_final: 0.6607 (ttm) REVERT: B 553 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.5846 (ttp) REVERT: B 656 MET cc_start: 0.7379 (tpp) cc_final: 0.6644 (tpt) REVERT: B 714 GLN cc_start: 0.7911 (mt0) cc_final: 0.7682 (mt0) REVERT: B 783 MET cc_start: 0.3439 (mmm) cc_final: 0.3003 (mmm) REVERT: B 807 TYR cc_start: 0.7883 (m-80) cc_final: 0.7629 (m-80) REVERT: B 844 LYS cc_start: 0.7597 (tppt) cc_final: 0.7082 (mmtm) REVERT: B 890 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7370 (tt) REVERT: C 68 GLU cc_start: 0.6518 (mp0) cc_final: 0.5760 (mp0) REVERT: C 213 GLU cc_start: 0.7414 (tt0) cc_final: 0.7174 (tt0) REVERT: C 356 TYR cc_start: 0.6547 (t80) cc_final: 0.6251 (t80) REVERT: C 363 ARG cc_start: 0.7421 (mmt180) cc_final: 0.6976 (mmt-90) REVERT: C 423 GLU cc_start: 0.7264 (mp0) cc_final: 0.6923 (mp0) REVERT: C 467 TYR cc_start: 0.7516 (m-10) cc_final: 0.7146 (m-80) REVERT: C 589 ASN cc_start: 0.6129 (m-40) cc_final: 0.5762 (m-40) REVERT: C 602 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7645 (mmtt) REVERT: C 769 LYS cc_start: 0.7860 (tmmt) cc_final: 0.7442 (tmtt) REVERT: C 826 THR cc_start: 0.8137 (m) cc_final: 0.7655 (p) REVERT: C 849 GLU cc_start: 0.7147 (mp0) cc_final: 0.5840 (mm-30) outliers start: 76 outliers final: 51 residues processed: 564 average time/residue: 0.3374 time to fit residues: 299.3945 Evaluate side-chains 557 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 501 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 204 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 204 ASN A 415 ASN A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 604 ASN B 773 GLN C 228 GLN C 273 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23934 Z= 0.194 Angle : 0.577 11.547 32442 Z= 0.292 Chirality : 0.042 0.337 3873 Planarity : 0.004 0.055 4066 Dihedral : 6.595 149.231 3289 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.00 % Allowed : 16.49 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.18 (0.15), residues: 3048 helix: 1.63 (0.13), residues: 1656 sheet: -0.11 (0.23), residues: 456 loop : -0.17 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 800 HIS 0.002 0.000 HIS A 991 PHE 0.026 0.001 PHE A 517 TYR 0.026 0.001 TYR C 848 ARG 0.006 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 522 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6526 (mm-30) REVERT: A 99 ASP cc_start: 0.5235 (OUTLIER) cc_final: 0.4684 (p0) REVERT: A 213 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6467 (mt-10) REVERT: A 304 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6781 (pt0) REVERT: A 435 MET cc_start: 0.4884 (mmm) cc_final: 0.4667 (mmm) REVERT: A 572 SER cc_start: 0.8165 (t) cc_final: 0.7768 (m) REVERT: A 684 MET cc_start: 0.7254 (mpp) cc_final: 0.5254 (mmm) REVERT: A 693 GLU cc_start: 0.7345 (tp30) cc_final: 0.6970 (tp30) REVERT: A 769 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6313 (ttpt) REVERT: A 884 GLU cc_start: 0.6639 (mp0) cc_final: 0.6421 (mp0) REVERT: A 939 PHE cc_start: 0.6341 (m-80) cc_final: 0.5922 (t80) REVERT: B 1 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5370 (ptt) REVERT: B 165 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6909 (mm-30) REVERT: B 184 MET cc_start: 0.5926 (mmp) cc_final: 0.5499 (mmm) REVERT: B 518 ASP cc_start: 0.6448 (t0) cc_final: 0.6238 (t0) REVERT: B 522 LYS cc_start: 0.7516 (mtmm) cc_final: 0.7158 (mtmm) REVERT: B 527 MET cc_start: 0.6926 (ttt) cc_final: 0.6611 (ttm) REVERT: B 656 MET cc_start: 0.7278 (tpp) cc_final: 0.6589 (tpt) REVERT: B 679 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7343 (mtt180) REVERT: B 714 GLN cc_start: 0.7966 (mt0) cc_final: 0.7686 (mt0) REVERT: B 783 MET cc_start: 0.3462 (mmm) cc_final: 0.3089 (mmm) REVERT: B 807 TYR cc_start: 0.7705 (m-80) cc_final: 0.7420 (m-80) REVERT: B 890 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7338 (tt) REVERT: C 68 GLU cc_start: 0.6343 (mp0) cc_final: 0.5576 (mp0) REVERT: C 213 GLU cc_start: 0.7429 (tt0) cc_final: 0.7171 (tt0) REVERT: C 356 TYR cc_start: 0.6466 (t80) cc_final: 0.6192 (t80) REVERT: C 363 ARG cc_start: 0.7405 (mmt180) cc_final: 0.6939 (mmt-90) REVERT: C 423 GLU cc_start: 0.7287 (mp0) cc_final: 0.6959 (mp0) REVERT: C 463 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7526 (m) REVERT: C 589 ASN cc_start: 0.6094 (m-40) cc_final: 0.5719 (m-40) REVERT: C 769 LYS cc_start: 0.7789 (tmmt) cc_final: 0.7379 (tmtt) REVERT: C 826 THR cc_start: 0.8221 (m) cc_final: 0.7704 (p) REVERT: C 849 GLU cc_start: 0.7004 (mp0) cc_final: 0.6325 (mp0) outliers start: 77 outliers final: 46 residues processed: 563 average time/residue: 0.3243 time to fit residues: 288.4201 Evaluate side-chains 556 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 503 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 20.0000 chunk 266 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 296 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 415 ASN B 604 ASN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23934 Z= 0.368 Angle : 0.656 11.330 32442 Z= 0.338 Chirality : 0.045 0.319 3873 Planarity : 0.005 0.065 4066 Dihedral : 6.822 141.085 3289 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.74 % Allowed : 16.76 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3048 helix: 1.44 (0.13), residues: 1653 sheet: -0.13 (0.24), residues: 433 loop : -0.41 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 800 HIS 0.003 0.001 HIS C 360 PHE 0.025 0.002 PHE A 517 TYR 0.026 0.002 TYR C 848 ARG 0.005 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 520 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6625 (mm-30) REVERT: A 99 ASP cc_start: 0.5246 (OUTLIER) cc_final: 0.4716 (p0) REVERT: A 138 MET cc_start: 0.7931 (ptm) cc_final: 0.7656 (ptm) REVERT: A 154 LEU cc_start: 0.8465 (mt) cc_final: 0.8166 (mp) REVERT: A 156 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7306 (t70) REVERT: A 164 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6357 (mt-10) REVERT: A 304 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: A 398 MET cc_start: 0.7851 (mtm) cc_final: 0.7554 (mtm) REVERT: A 435 MET cc_start: 0.4887 (mmm) cc_final: 0.4676 (mmm) REVERT: A 638 LYS cc_start: 0.7706 (tptp) cc_final: 0.7386 (mmtt) REVERT: A 676 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5434 (mm) REVERT: A 684 MET cc_start: 0.7369 (mpp) cc_final: 0.5381 (mmm) REVERT: A 693 GLU cc_start: 0.7384 (tp30) cc_final: 0.6961 (tp30) REVERT: A 769 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6289 (ttpt) REVERT: A 939 PHE cc_start: 0.6456 (m-80) cc_final: 0.6036 (t80) REVERT: B 1 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5016 (ptt) REVERT: B 5 PHE cc_start: 0.8569 (m-80) cc_final: 0.8353 (m-80) REVERT: B 182 LYS cc_start: 0.6655 (mtmm) cc_final: 0.6446 (mtmm) REVERT: B 184 MET cc_start: 0.6104 (mmp) cc_final: 0.5801 (mmm) REVERT: B 522 LYS cc_start: 0.7553 (mtmm) cc_final: 0.7142 (mtmm) REVERT: B 527 MET cc_start: 0.6876 (ttt) cc_final: 0.6570 (ttm) REVERT: B 638 LYS cc_start: 0.7258 (tmtt) cc_final: 0.6967 (tmmt) REVERT: B 654 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6348 (mt-10) REVERT: B 656 MET cc_start: 0.7568 (tpp) cc_final: 0.6774 (tpt) REVERT: B 714 GLN cc_start: 0.7952 (mt0) cc_final: 0.7724 (mt0) REVERT: B 783 MET cc_start: 0.3438 (mmm) cc_final: 0.3057 (mmm) REVERT: B 890 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 939 PHE cc_start: 0.7505 (t80) cc_final: 0.7239 (t80) REVERT: C 68 GLU cc_start: 0.6517 (mp0) cc_final: 0.5758 (mp0) REVERT: C 213 GLU cc_start: 0.7496 (tt0) cc_final: 0.7245 (tt0) REVERT: C 356 TYR cc_start: 0.6513 (t80) cc_final: 0.6249 (t80) REVERT: C 363 ARG cc_start: 0.7539 (mmt180) cc_final: 0.7059 (mmt-90) REVERT: C 423 GLU cc_start: 0.7332 (mp0) cc_final: 0.6913 (mp0) REVERT: C 463 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7790 (m) REVERT: C 467 TYR cc_start: 0.7453 (m-80) cc_final: 0.7187 (m-80) REVERT: C 769 LYS cc_start: 0.7853 (tmmt) cc_final: 0.7371 (tmtt) REVERT: C 826 THR cc_start: 0.8192 (m) cc_final: 0.7663 (p) REVERT: C 849 GLU cc_start: 0.7231 (mp0) cc_final: 0.5800 (mm-30) outliers start: 96 outliers final: 71 residues processed: 567 average time/residue: 0.3350 time to fit residues: 301.3101 Evaluate side-chains 587 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 506 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 753 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 167 optimal weight: 0.7980 chunk 249 optimal weight: 0.0980 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 415 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 176 GLN B 360 HIS B 604 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 773 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23934 Z= 0.178 Angle : 0.581 13.985 32442 Z= 0.295 Chirality : 0.042 0.347 3873 Planarity : 0.004 0.064 4066 Dihedral : 6.240 138.444 3286 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.57 % Allowed : 18.79 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.13 (0.15), residues: 3048 helix: 1.59 (0.13), residues: 1645 sheet: -0.01 (0.24), residues: 438 loop : -0.23 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 800 HIS 0.001 0.000 HIS A 991 PHE 0.022 0.001 PHE A 517 TYR 0.024 0.001 TYR C 848 ARG 0.006 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 516 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7228 (pt) cc_final: 0.7010 (pt) REVERT: A 68 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6653 (mm-30) REVERT: A 99 ASP cc_start: 0.5117 (p0) cc_final: 0.4579 (p0) REVERT: A 164 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6368 (mt-10) REVERT: A 304 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6589 (tt0) REVERT: A 357 LEU cc_start: 0.7985 (mm) cc_final: 0.7646 (mm) REVERT: A 398 MET cc_start: 0.7737 (mtm) cc_final: 0.7410 (mtm) REVERT: A 435 MET cc_start: 0.4928 (mmm) cc_final: 0.4702 (mmm) REVERT: A 456 MET cc_start: 0.8034 (ptm) cc_final: 0.7570 (ptm) REVERT: A 572 SER cc_start: 0.8100 (t) cc_final: 0.7729 (m) REVERT: A 676 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5491 (mm) REVERT: A 684 MET cc_start: 0.7339 (mpp) cc_final: 0.5298 (mmm) REVERT: A 693 GLU cc_start: 0.7377 (tp30) cc_final: 0.6938 (tp30) REVERT: A 769 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6338 (ttpt) REVERT: A 939 PHE cc_start: 0.6286 (m-80) cc_final: 0.5898 (t80) REVERT: B 1 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5241 (ptt) REVERT: B 321 MET cc_start: 0.5308 (mtt) cc_final: 0.5093 (mtt) REVERT: B 522 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7386 (mtmm) REVERT: B 527 MET cc_start: 0.6888 (ttt) cc_final: 0.6539 (ttm) REVERT: B 654 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6258 (mt-10) REVERT: B 656 MET cc_start: 0.7271 (tpp) cc_final: 0.6669 (tpt) REVERT: B 714 GLN cc_start: 0.7918 (mt0) cc_final: 0.7671 (mt0) REVERT: B 771 ARG cc_start: 0.7915 (ptt90) cc_final: 0.7680 (ptt90) REVERT: B 783 MET cc_start: 0.3524 (mmm) cc_final: 0.3205 (mmm) REVERT: B 844 LYS cc_start: 0.7525 (tppt) cc_final: 0.7010 (mmtm) REVERT: B 890 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7344 (tt) REVERT: B 939 PHE cc_start: 0.7340 (t80) cc_final: 0.7121 (t80) REVERT: C 68 GLU cc_start: 0.6127 (mp0) cc_final: 0.5439 (mp0) REVERT: C 356 TYR cc_start: 0.6369 (t80) cc_final: 0.6067 (t80) REVERT: C 363 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7021 (mmt-90) REVERT: C 423 GLU cc_start: 0.7306 (mp0) cc_final: 0.6933 (mp0) REVERT: C 769 LYS cc_start: 0.7718 (tmmt) cc_final: 0.7280 (tmtt) REVERT: C 771 ARG cc_start: 0.7396 (ptt90) cc_final: 0.7002 (ptt-90) REVERT: C 826 THR cc_start: 0.8222 (m) cc_final: 0.7728 (p) REVERT: C 849 GLU cc_start: 0.7077 (mp0) cc_final: 0.5777 (mm-30) outliers start: 66 outliers final: 42 residues processed: 549 average time/residue: 0.3386 time to fit residues: 295.4723 Evaluate side-chains 554 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 505 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 268 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 228 GLN A 237 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 604 ASN C 228 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23934 Z= 0.344 Angle : 0.666 12.476 32442 Z= 0.341 Chirality : 0.045 0.330 3873 Planarity : 0.005 0.070 4066 Dihedral : 6.506 130.985 3286 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.85 % Allowed : 19.34 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3048 helix: 1.45 (0.13), residues: 1645 sheet: -0.17 (0.24), residues: 438 loop : -0.38 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 800 HIS 0.003 0.001 HIS C 360 PHE 0.022 0.002 PHE A 517 TYR 0.027 0.002 TYR C 467 ARG 0.005 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 518 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6629 (mm-30) REVERT: A 99 ASP cc_start: 0.5150 (p0) cc_final: 0.4586 (p0) REVERT: A 104 GLN cc_start: 0.7738 (tt0) cc_final: 0.7488 (tt0) REVERT: A 154 LEU cc_start: 0.8425 (mt) cc_final: 0.8166 (mp) REVERT: A 164 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6345 (mt-10) REVERT: A 304 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6743 (tt0) REVERT: A 357 LEU cc_start: 0.8034 (mm) cc_final: 0.7726 (mm) REVERT: A 398 MET cc_start: 0.7874 (mtm) cc_final: 0.7576 (mtm) REVERT: A 638 LYS cc_start: 0.7721 (tptp) cc_final: 0.7263 (mmmt) REVERT: A 676 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5402 (mm) REVERT: A 684 MET cc_start: 0.7372 (mpp) cc_final: 0.5366 (mmm) REVERT: A 693 GLU cc_start: 0.7392 (tp30) cc_final: 0.6903 (tp30) REVERT: A 769 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6373 (ttpt) REVERT: A 939 PHE cc_start: 0.6269 (m-80) cc_final: 0.5872 (t80) REVERT: B 1 MET cc_start: 0.5860 (ptt) cc_final: 0.5074 (ptt) REVERT: B 5 PHE cc_start: 0.8557 (m-80) cc_final: 0.8349 (m-80) REVERT: B 522 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7412 (mtmm) REVERT: B 527 MET cc_start: 0.6891 (ttt) cc_final: 0.6575 (ttm) REVERT: B 564 GLU cc_start: 0.8182 (tp30) cc_final: 0.7487 (tp30) REVERT: B 638 LYS cc_start: 0.7355 (tmtt) cc_final: 0.6659 (tptp) REVERT: B 654 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: B 656 MET cc_start: 0.7573 (tpp) cc_final: 0.6787 (tpt) REVERT: B 714 GLN cc_start: 0.7942 (mt0) cc_final: 0.7701 (mt0) REVERT: B 771 ARG cc_start: 0.7982 (ptt90) cc_final: 0.7739 (ptt90) REVERT: B 783 MET cc_start: 0.3517 (mmm) cc_final: 0.3180 (mmm) REVERT: B 807 TYR cc_start: 0.7890 (m-80) cc_final: 0.7659 (m-80) REVERT: B 844 LYS cc_start: 0.7677 (tppt) cc_final: 0.7039 (mmtm) REVERT: B 890 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7726 (tt) REVERT: B 939 PHE cc_start: 0.7494 (t80) cc_final: 0.7205 (t80) REVERT: C 68 GLU cc_start: 0.6485 (mp0) cc_final: 0.5728 (mp0) REVERT: C 356 TYR cc_start: 0.6555 (t80) cc_final: 0.6308 (t80) REVERT: C 363 ARG cc_start: 0.7650 (mmt180) cc_final: 0.7109 (mmt-90) REVERT: C 423 GLU cc_start: 0.7319 (mp0) cc_final: 0.6903 (mp0) REVERT: C 602 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7427 (mmtt) REVERT: C 769 LYS cc_start: 0.7781 (tmmt) cc_final: 0.7355 (tmtt) REVERT: C 771 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7216 (ptt-90) REVERT: C 826 THR cc_start: 0.8192 (m) cc_final: 0.7674 (p) REVERT: C 849 GLU cc_start: 0.7249 (mp0) cc_final: 0.5736 (mm-30) outliers start: 73 outliers final: 54 residues processed: 554 average time/residue: 0.3243 time to fit residues: 283.9342 Evaluate side-chains 563 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 503 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 753 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 180 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 604 ASN C 282 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23934 Z= 0.266 Angle : 0.641 12.356 32442 Z= 0.325 Chirality : 0.043 0.344 3873 Planarity : 0.005 0.071 4066 Dihedral : 6.341 127.275 3286 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.92 % Allowed : 19.69 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3048 helix: 1.47 (0.13), residues: 1644 sheet: -0.11 (0.24), residues: 436 loop : -0.38 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 800 HIS 0.002 0.000 HIS C 360 PHE 0.020 0.001 PHE A 517 TYR 0.036 0.002 TYR C 467 ARG 0.006 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 502 time to evaluate : 2.430 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: A 68 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6603 (mm-30) REVERT: A 99 ASP cc_start: 0.5019 (p0) cc_final: 0.4523 (p0) REVERT: A 154 LEU cc_start: 0.8465 (mt) cc_final: 0.8160 (mp) REVERT: A 156 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7243 (t70) REVERT: A 164 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6312 (mt-10) REVERT: A 304 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: A 357 LEU cc_start: 0.7949 (mm) cc_final: 0.7646 (mm) REVERT: A 398 MET cc_start: 0.7824 (mtm) cc_final: 0.7501 (mtm) REVERT: A 639 MET cc_start: 0.6719 (mmm) cc_final: 0.6467 (ttt) REVERT: A 676 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5449 (mm) REVERT: A 693 GLU cc_start: 0.7391 (tp30) cc_final: 0.6977 (tm-30) REVERT: A 697 MET cc_start: 0.7578 (mpp) cc_final: 0.6915 (mmt) REVERT: A 769 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6373 (ttpt) REVERT: A 939 PHE cc_start: 0.6232 (m-80) cc_final: 0.5836 (t80) REVERT: B 1 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4782 (ptt) REVERT: B 5 PHE cc_start: 0.8526 (m-80) cc_final: 0.8323 (m-80) REVERT: B 182 LYS cc_start: 0.6435 (mtmm) cc_final: 0.5920 (ptpp) REVERT: B 522 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7399 (mtmm) REVERT: B 527 MET cc_start: 0.6924 (ttt) cc_final: 0.6618 (ttm) REVERT: B 564 GLU cc_start: 0.8105 (tp30) cc_final: 0.7430 (tp30) REVERT: B 638 LYS cc_start: 0.7254 (tmtt) cc_final: 0.6612 (tptp) REVERT: B 654 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6434 (mt-10) REVERT: B 656 MET cc_start: 0.7475 (tpp) cc_final: 0.6744 (tpt) REVERT: B 714 GLN cc_start: 0.7963 (mt0) cc_final: 0.7709 (mt0) REVERT: B 771 ARG cc_start: 0.7967 (ptt90) cc_final: 0.7659 (ptt90) REVERT: B 783 MET cc_start: 0.3479 (mmm) cc_final: 0.3150 (mmm) REVERT: B 807 TYR cc_start: 0.7891 (m-80) cc_final: 0.7680 (m-80) REVERT: B 844 LYS cc_start: 0.7577 (tppt) cc_final: 0.7020 (mmtm) REVERT: B 890 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 939 PHE cc_start: 0.7473 (t80) cc_final: 0.7171 (t80) REVERT: C 68 GLU cc_start: 0.6279 (mp0) cc_final: 0.5587 (mp0) REVERT: C 356 TYR cc_start: 0.6497 (t80) cc_final: 0.6246 (t80) REVERT: C 363 ARG cc_start: 0.7664 (mmt180) cc_final: 0.7098 (mmt-90) REVERT: C 423 GLU cc_start: 0.7339 (mp0) cc_final: 0.6908 (mp0) REVERT: C 602 LYS cc_start: 0.7812 (mmtt) cc_final: 0.7415 (mmtt) REVERT: C 769 LYS cc_start: 0.7762 (tmmt) cc_final: 0.7321 (tmtt) REVERT: C 771 ARG cc_start: 0.7553 (ptt90) cc_final: 0.7267 (ptt-90) REVERT: C 826 THR cc_start: 0.8255 (m) cc_final: 0.7736 (p) REVERT: C 849 GLU cc_start: 0.7145 (mp0) cc_final: 0.5643 (mm-30) outliers start: 75 outliers final: 57 residues processed: 539 average time/residue: 0.3665 time to fit residues: 314.5698 Evaluate side-chains 563 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 498 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 202 optimal weight: 0.0670 chunk 304 optimal weight: 0.4980 chunk 280 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 415 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN C 282 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN C 773 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23934 Z= 0.178 Angle : 0.616 13.613 32442 Z= 0.309 Chirality : 0.042 0.346 3873 Planarity : 0.005 0.068 4066 Dihedral : 6.022 124.141 3286 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.34 % Allowed : 20.58 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.13 (0.16), residues: 3048 helix: 1.59 (0.13), residues: 1645 sheet: 0.08 (0.24), residues: 436 loop : -0.28 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 800 HIS 0.001 0.000 HIS B 360 PHE 0.019 0.001 PHE A 517 TYR 0.045 0.001 TYR C 467 ARG 0.007 0.000 ARG B 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 509 time to evaluate : 2.332 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 68 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6625 (mm-30) REVERT: A 99 ASP cc_start: 0.4998 (p0) cc_final: 0.4505 (p0) REVERT: A 104 GLN cc_start: 0.7687 (tt0) cc_final: 0.7344 (tt0) REVERT: A 164 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6339 (mt-10) REVERT: A 304 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6574 (tt0) REVERT: A 357 LEU cc_start: 0.7940 (mm) cc_final: 0.7654 (mm) REVERT: A 398 MET cc_start: 0.7760 (mtm) cc_final: 0.7383 (mtm) REVERT: A 572 SER cc_start: 0.7995 (t) cc_final: 0.7652 (m) REVERT: A 590 GLN cc_start: 0.5148 (tp-100) cc_final: 0.4728 (tp-100) REVERT: A 627 LYS cc_start: 0.6630 (mmtt) cc_final: 0.6230 (mmtp) REVERT: A 676 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5490 (mm) REVERT: A 693 GLU cc_start: 0.7378 (tp30) cc_final: 0.7126 (tp30) REVERT: A 697 MET cc_start: 0.7477 (mpp) cc_final: 0.7025 (mmp) REVERT: A 769 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6379 (ttpt) REVERT: B 1 MET cc_start: 0.5855 (OUTLIER) cc_final: 0.5391 (ptt) REVERT: B 115 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5494 (pp20) REVERT: B 522 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7392 (mtmm) REVERT: B 527 MET cc_start: 0.6852 (ttt) cc_final: 0.6533 (ttm) REVERT: B 564 GLU cc_start: 0.8018 (tp30) cc_final: 0.7513 (tp30) REVERT: B 631 GLU cc_start: 0.6623 (tp30) cc_final: 0.6394 (tp30) REVERT: B 654 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6571 (mt-10) REVERT: B 656 MET cc_start: 0.7302 (tpp) cc_final: 0.6731 (tpt) REVERT: B 714 GLN cc_start: 0.7911 (mt0) cc_final: 0.7647 (mt0) REVERT: B 771 ARG cc_start: 0.7881 (ptt90) cc_final: 0.7611 (ptt90) REVERT: B 783 MET cc_start: 0.3561 (mmm) cc_final: 0.3211 (mmm) REVERT: B 844 LYS cc_start: 0.7591 (tppt) cc_final: 0.7004 (mmtm) REVERT: B 890 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7354 (tt) REVERT: B 939 PHE cc_start: 0.7299 (t80) cc_final: 0.7083 (t80) REVERT: C 68 GLU cc_start: 0.6041 (mp0) cc_final: 0.5363 (mp0) REVERT: C 356 TYR cc_start: 0.6359 (t80) cc_final: 0.6017 (t80) REVERT: C 363 ARG cc_start: 0.7633 (mmt180) cc_final: 0.7084 (mmt-90) REVERT: C 423 GLU cc_start: 0.7347 (mp0) cc_final: 0.6922 (mp0) REVERT: C 466 ILE cc_start: 0.8641 (mt) cc_final: 0.8320 (mm) REVERT: C 602 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7389 (mmtt) REVERT: C 745 MET cc_start: 0.7876 (tpp) cc_final: 0.7402 (tpp) REVERT: C 769 LYS cc_start: 0.7747 (tmmt) cc_final: 0.7307 (tmtt) REVERT: C 771 ARG cc_start: 0.7543 (ptt90) cc_final: 0.7291 (ptt-90) REVERT: C 826 THR cc_start: 0.8172 (m) cc_final: 0.7663 (p) REVERT: C 849 GLU cc_start: 0.7051 (mp0) cc_final: 0.5647 (mm-30) outliers start: 60 outliers final: 44 residues processed: 536 average time/residue: 0.3318 time to fit residues: 280.9250 Evaluate side-chains 552 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 500 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 973 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 249 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 248 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN C 282 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.178562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.148066 restraints weight = 27362.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.147605 restraints weight = 32397.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.149407 restraints weight = 30582.786| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23934 Z= 0.200 Angle : 0.622 12.982 32442 Z= 0.312 Chirality : 0.042 0.320 3873 Planarity : 0.005 0.068 4066 Dihedral : 5.943 120.524 3286 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.26 % Allowed : 20.62 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.18 (0.15), residues: 3048 helix: 1.64 (0.13), residues: 1639 sheet: 0.16 (0.24), residues: 454 loop : -0.29 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 800 HIS 0.002 0.000 HIS B 360 PHE 0.018 0.001 PHE A 517 TYR 0.039 0.001 TYR C 467 ARG 0.006 0.000 ARG B 418 =============================================================================== Job complete usr+sys time: 5445.85 seconds wall clock time: 99 minutes 27.23 seconds (5967.23 seconds total)