Starting phenix.real_space_refine on Sat Mar 23 19:32:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ny1_12644/03_2024/7ny1_12644_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ny1_12644/03_2024/7ny1_12644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ny1_12644/03_2024/7ny1_12644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ny1_12644/03_2024/7ny1_12644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ny1_12644/03_2024/7ny1_12644_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ny1_12644/03_2024/7ny1_12644_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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: 7 Type Number sf(0) Gaussians K 6 8.98 5 P 12 5.49 5 Mg 6 5.21 5 S 138 5.16 5 C 24780 2.51 5 N 6360 2.21 5 O 7128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 739": "OD1" <-> "OD2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 900": "NH1" <-> "NH2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ARG 508": "NH1" <-> "NH2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B ASP 539": "OD1" <-> "OD2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B ASP 638": "OD1" <-> "OD2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 739": "OD1" <-> "OD2" Residue "B GLU 782": "OE1" <-> "OE2" Residue "B ARG 813": "NH1" <-> "NH2" Residue "B PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 859": "NH1" <-> "NH2" Residue "B ARG 900": "NH1" <-> "NH2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 519": "NH1" <-> "NH2" Residue "C ASP 539": "OD1" <-> "OD2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C GLU 602": "OE1" <-> "OE2" Residue "C GLU 620": "OE1" <-> "OE2" Residue "C ASP 638": "OD1" <-> "OD2" Residue "C ARG 682": "NH1" <-> "NH2" Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C GLU 782": "OE1" <-> "OE2" Residue "C ARG 813": "NH1" <-> "NH2" Residue "C PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 859": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C GLU 903": "OE1" <-> "OE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D ASP 423": "OD1" <-> "OD2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 519": "NH1" <-> "NH2" Residue "D ASP 539": "OD1" <-> "OD2" Residue "D GLU 567": "OE1" <-> "OE2" Residue "D ARG 583": "NH1" <-> "NH2" Residue "D GLU 602": "OE1" <-> "OE2" Residue "D GLU 620": "OE1" <-> "OE2" Residue "D ASP 638": "OD1" <-> "OD2" Residue "D ARG 682": "NH1" <-> "NH2" Residue "D TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 739": "OD1" <-> "OD2" Residue "D GLU 782": "OE1" <-> "OE2" Residue "D ARG 813": "NH1" <-> "NH2" Residue "D PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 859": "NH1" <-> "NH2" Residue "D ARG 900": "NH1" <-> "NH2" Residue "D GLU 903": "OE1" <-> "OE2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E ARG 315": "NH1" <-> "NH2" Residue "E GLU 367": "OE1" <-> "OE2" Residue "E GLU 373": "OE1" <-> "OE2" Residue "E ASP 423": "OD1" <-> "OD2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "E TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "E ARG 508": "NH1" <-> "NH2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 519": "NH1" <-> "NH2" Residue "E ASP 539": "OD1" <-> "OD2" Residue "E GLU 567": "OE1" <-> "OE2" Residue "E ARG 583": "NH1" <-> "NH2" Residue "E GLU 602": "OE1" <-> "OE2" Residue "E GLU 620": "OE1" <-> "OE2" Residue "E ASP 638": "OD1" <-> "OD2" Residue "E ARG 682": "NH1" <-> "NH2" Residue "E TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 739": "OD1" <-> "OD2" Residue "E GLU 782": "OE1" <-> "OE2" Residue "E ARG 813": "NH1" <-> "NH2" Residue "E PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 859": "NH1" <-> "NH2" Residue "E ARG 900": "NH1" <-> "NH2" Residue "E GLU 903": "OE1" <-> "OE2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 373": "OE1" <-> "OE2" Residue "F ASP 423": "OD1" <-> "OD2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 504": "OE1" <-> "OE2" Residue "F ARG 508": "NH1" <-> "NH2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 519": "NH1" <-> "NH2" Residue "F ASP 539": "OD1" <-> "OD2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ARG 583": "NH1" <-> "NH2" Residue "F GLU 602": "OE1" <-> "OE2" Residue "F GLU 620": "OE1" <-> "OE2" Residue "F ASP 638": "OD1" <-> "OD2" Residue "F ARG 682": "NH1" <-> "NH2" Residue "F TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 739": "OD1" <-> "OD2" Residue "F GLU 782": "OE1" <-> "OE2" Residue "F ARG 813": "NH1" <-> "NH2" Residue "F PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 859": "NH1" <-> "NH2" Residue "F ARG 900": "NH1" <-> "NH2" Residue "F GLU 903": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38430 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "B" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "C" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "D" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "E" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "F" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.08, per 1000 atoms: 0.50 Number of scatterers: 38430 At special positions: 0 Unit cell: (186.651, 168.237, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 6 19.00 S 138 16.00 P 12 15.00 Mg 6 11.99 O 7128 8.00 N 6360 7.00 C 24780 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: 15.75 Conformation dependent library (CDL) restraints added in 6.9 seconds 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 36 sheets defined 48.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.62 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.732A pdb=" N PHE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 143 through 176 removed outlier: 3.857A pdb=" N ASP A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 314 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.571A pdb=" N ILE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.572A pdb=" N ALA A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.929A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.635A pdb=" N LEU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.518A pdb=" N GLN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.850A pdb=" N THR A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 Processing helix chain 'A' and resid 581 through 584 No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 594 through 602 removed outlier: 3.822A pdb=" N ASP A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.746A pdb=" N TYR A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 671 through 713 removed outlier: 3.993A pdb=" N LEU A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 752 through 780 removed outlier: 3.686A pdb=" N MET A 777 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 812 removed outlier: 3.686A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 810 " --> pdb=" O ASN A 806 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 811 " --> pdb=" O TRP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 844 Processing helix chain 'A' and resid 854 through 879 removed outlier: 3.661A pdb=" N VAL A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 918 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.732A pdb=" N PHE B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 143 through 176 removed outlier: 3.857A pdb=" N ASP B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 338 through 355 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.571A pdb=" N ILE B 366 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.572A pdb=" N ALA B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 428 removed outlier: 3.929A pdb=" N ALA B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.635A pdb=" N LEU B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 507 removed outlier: 3.517A pdb=" N GLN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.850A pdb=" N THR B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 Processing helix chain 'B' and resid 581 through 584 No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 594 through 602 removed outlier: 3.822A pdb=" N ASP B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.745A pdb=" N TYR B 616 " --> pdb=" O PRO B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 671 through 713 removed outlier: 3.993A pdb=" N LEU B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 731 Processing helix chain 'B' and resid 752 through 780 removed outlier: 3.686A pdb=" N MET B 777 " --> pdb=" O THR B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 812 removed outlier: 3.686A pdb=" N LEU B 808 " --> pdb=" O THR B 804 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 809 " --> pdb=" O GLU B 805 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE B 810 " --> pdb=" O ASN B 806 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 811 " --> pdb=" O TRP B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 844 Processing helix chain 'B' and resid 854 through 879 removed outlier: 3.660A pdb=" N VAL B 858 " --> pdb=" O ILE B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 918 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 114 through 120 removed outlier: 3.733A pdb=" N PHE C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 133 Processing helix chain 'C' and resid 143 through 176 removed outlier: 3.857A pdb=" N ASP C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 338 through 355 Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.571A pdb=" N ILE C 366 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.572A pdb=" N ALA C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 removed outlier: 3.929A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 483 removed outlier: 3.635A pdb=" N LEU C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 507 removed outlier: 3.518A pdb=" N GLN C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 549 removed outlier: 3.850A pdb=" N THR C 549 " --> pdb=" O CYS C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 Processing helix chain 'C' and resid 581 through 584 No H-bonds generated for 'chain 'C' and resid 581 through 584' Processing helix chain 'C' and resid 594 through 602 removed outlier: 3.823A pdb=" N ASP C 599 " --> pdb=" O SER C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 624 removed outlier: 3.746A pdb=" N TYR C 616 " --> pdb=" O PRO C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 644 Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 671 through 713 removed outlier: 3.993A pdb=" N LEU C 708 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 731 Processing helix chain 'C' and resid 752 through 780 removed outlier: 3.686A pdb=" N MET C 777 " --> pdb=" O THR C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 812 removed outlier: 3.686A pdb=" N LEU C 808 " --> pdb=" O THR C 804 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 809 " --> pdb=" O GLU C 805 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE C 810 " --> pdb=" O ASN C 806 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE C 811 " --> pdb=" O TRP C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 844 Processing helix chain 'C' and resid 854 through 879 removed outlier: 3.661A pdb=" N VAL C 858 " --> pdb=" O ILE C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 918 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 114 through 120 removed outlier: 3.732A pdb=" N PHE D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 133 Processing helix chain 'D' and resid 143 through 176 removed outlier: 3.857A pdb=" N ASP D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 338 through 355 Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.571A pdb=" N ILE D 366 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.572A pdb=" N ALA D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 428 removed outlier: 3.929A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 removed outlier: 3.635A pdb=" N LEU D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 507 removed outlier: 3.518A pdb=" N GLN D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 497 " --> pdb=" O GLU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 549 removed outlier: 3.850A pdb=" N THR D 549 " --> pdb=" O CYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 581 through 584 No H-bonds generated for 'chain 'D' and resid 581 through 584' Processing helix chain 'D' and resid 594 through 602 removed outlier: 3.822A pdb=" N ASP D 599 " --> pdb=" O SER D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 624 removed outlier: 3.746A pdb=" N TYR D 616 " --> pdb=" O PRO D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 644 Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 671 through 713 removed outlier: 3.993A pdb=" N LEU D 708 " --> pdb=" O ILE D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 731 Processing helix chain 'D' and resid 752 through 780 removed outlier: 3.686A pdb=" N MET D 777 " --> pdb=" O THR D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 812 removed outlier: 3.686A pdb=" N LEU D 808 " --> pdb=" O THR D 804 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 809 " --> pdb=" O GLU D 805 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE D 810 " --> pdb=" O ASN D 806 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 811 " --> pdb=" O TRP D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 844 Processing helix chain 'D' and resid 854 through 879 removed outlier: 3.661A pdb=" N VAL D 858 " --> pdb=" O ILE D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 918 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 114 through 120 removed outlier: 3.732A pdb=" N PHE E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 133 Processing helix chain 'E' and resid 143 through 176 removed outlier: 3.857A pdb=" N ASP E 170 " --> pdb=" O GLY E 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 314 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 338 through 355 Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.571A pdb=" N ILE E 366 " --> pdb=" O LEU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 411 removed outlier: 3.572A pdb=" N ALA E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 428 removed outlier: 3.929A pdb=" N ALA E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 483 removed outlier: 3.635A pdb=" N LEU E 481 " --> pdb=" O PRO E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 507 removed outlier: 3.517A pdb=" N GLN E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 549 removed outlier: 3.850A pdb=" N THR E 549 " --> pdb=" O CYS E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 572 Processing helix chain 'E' and resid 581 through 584 No H-bonds generated for 'chain 'E' and resid 581 through 584' Processing helix chain 'E' and resid 594 through 602 removed outlier: 3.822A pdb=" N ASP E 599 " --> pdb=" O SER E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 624 removed outlier: 3.745A pdb=" N TYR E 616 " --> pdb=" O PRO E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 644 Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'E' and resid 671 through 713 removed outlier: 3.993A pdb=" N LEU E 708 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 731 Processing helix chain 'E' and resid 752 through 780 removed outlier: 3.686A pdb=" N MET E 777 " --> pdb=" O THR E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 793 through 812 removed outlier: 3.686A pdb=" N LEU E 808 " --> pdb=" O THR E 804 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE E 809 " --> pdb=" O GLU E 805 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE E 810 " --> pdb=" O ASN E 806 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 811 " --> pdb=" O TRP E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 844 Processing helix chain 'E' and resid 854 through 879 removed outlier: 3.660A pdb=" N VAL E 858 " --> pdb=" O ILE E 854 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 918 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 114 through 120 removed outlier: 3.733A pdb=" N PHE F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 133 Processing helix chain 'F' and resid 143 through 176 removed outlier: 3.857A pdb=" N ASP F 170 " --> pdb=" O GLY F 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 314 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'F' and resid 338 through 355 Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.571A pdb=" N ILE F 366 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 411 removed outlier: 3.572A pdb=" N ALA F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.929A pdb=" N ALA F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 483 removed outlier: 3.635A pdb=" N LEU F 481 " --> pdb=" O PRO F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 507 removed outlier: 3.518A pdb=" N GLN F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 497 " --> pdb=" O GLU F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 549 removed outlier: 3.850A pdb=" N THR F 549 " --> pdb=" O CYS F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 572 Processing helix chain 'F' and resid 581 through 584 No H-bonds generated for 'chain 'F' and resid 581 through 584' Processing helix chain 'F' and resid 594 through 602 removed outlier: 3.823A pdb=" N ASP F 599 " --> pdb=" O SER F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 624 removed outlier: 3.746A pdb=" N TYR F 616 " --> pdb=" O PRO F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 644 Processing helix chain 'F' and resid 656 through 661 Processing helix chain 'F' and resid 671 through 713 removed outlier: 3.993A pdb=" N LEU F 708 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 731 Processing helix chain 'F' and resid 752 through 780 removed outlier: 3.686A pdb=" N MET F 777 " --> pdb=" O THR F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 812 removed outlier: 3.686A pdb=" N LEU F 808 " --> pdb=" O THR F 804 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE F 809 " --> pdb=" O GLU F 805 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE F 810 " --> pdb=" O ASN F 806 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE F 811 " --> pdb=" O TRP F 807 " (cutoff:3.500A) Processing helix chain 'F' and resid 825 through 844 Processing helix chain 'F' and resid 854 through 879 removed outlier: 3.661A pdb=" N VAL F 858 " --> pdb=" O ILE F 854 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 918 Processing sheet with id= A, first strand: chain 'A' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL A 204 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 256 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 214 through 216 Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 Processing sheet with id= D, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.667A pdb=" N ILE A 374 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 632 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 376 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER A 553 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER A 377 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS A 555 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 579 " --> pdb=" O GLY A 606 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 525 through 532 removed outlier: 3.937A pdb=" N GLU A 525 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 517 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 515 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 529 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A 513 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG A 511 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A 463 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 445 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.566A pdb=" N ARG A 253 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP A 226 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 251 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL B 204 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 256 " --> pdb=" O VAL B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 214 through 216 Processing sheet with id= I, first strand: chain 'B' and resid 358 through 360 Processing sheet with id= J, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.667A pdb=" N ILE B 374 " --> pdb=" O ALA B 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR B 632 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS B 376 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER B 553 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER B 377 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 555 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 579 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 525 through 532 removed outlier: 3.937A pdb=" N GLU B 525 " --> pdb=" O ARG B 517 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 517 " --> pdb=" O GLU B 525 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 515 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 529 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU B 513 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG B 511 " --> pdb=" O PRO B 531 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU B 463 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL B 445 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.565A pdb=" N ARG B 253 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 251 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL C 204 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 256 " --> pdb=" O VAL C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 214 through 216 Processing sheet with id= O, first strand: chain 'C' and resid 358 through 360 Processing sheet with id= P, first strand: chain 'C' and resid 647 through 650 removed outlier: 6.666A pdb=" N ILE C 374 " --> pdb=" O ALA C 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR C 632 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS C 376 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER C 553 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER C 377 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS C 555 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C 579 " --> pdb=" O GLY C 606 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 525 through 532 removed outlier: 3.937A pdb=" N GLU C 525 " --> pdb=" O ARG C 517 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 517 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 515 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 529 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU C 513 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 511 " --> pdb=" O PRO C 531 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 463 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL C 445 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 224 through 226 removed outlier: 3.565A pdb=" N ARG C 253 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP C 226 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 251 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL D 204 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 256 " --> pdb=" O VAL D 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 214 through 216 Processing sheet with id= U, first strand: chain 'D' and resid 358 through 360 Processing sheet with id= V, first strand: chain 'D' and resid 647 through 650 removed outlier: 6.667A pdb=" N ILE D 374 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR D 632 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS D 376 " --> pdb=" O THR D 632 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER D 553 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER D 377 " --> pdb=" O SER D 553 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS D 555 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR D 579 " --> pdb=" O GLY D 606 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 525 through 532 removed outlier: 3.937A pdb=" N GLU D 525 " --> pdb=" O ARG D 517 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 517 " --> pdb=" O GLU D 525 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 515 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE D 529 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU D 513 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG D 511 " --> pdb=" O PRO D 531 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU D 463 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 445 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 224 through 226 removed outlier: 3.566A pdb=" N ARG D 253 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP D 226 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL D 251 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL E 204 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA E 256 " --> pdb=" O VAL E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 214 through 216 Processing sheet with id= AA, first strand: chain 'E' and resid 358 through 360 Processing sheet with id= AB, first strand: chain 'E' and resid 647 through 650 removed outlier: 6.667A pdb=" N ILE E 374 " --> pdb=" O ALA E 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR E 632 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS E 376 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER E 553 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER E 377 " --> pdb=" O SER E 553 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS E 555 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR E 579 " --> pdb=" O GLY E 606 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 525 through 532 removed outlier: 3.937A pdb=" N GLU E 525 " --> pdb=" O ARG E 517 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG E 517 " --> pdb=" O GLU E 525 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL E 515 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE E 529 " --> pdb=" O LEU E 513 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU E 513 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG E 511 " --> pdb=" O PRO E 531 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU E 463 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL E 445 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 224 through 226 removed outlier: 3.565A pdb=" N ARG E 253 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP E 226 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL E 251 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL F 204 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA F 256 " --> pdb=" O VAL F 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'F' and resid 214 through 216 Processing sheet with id= AG, first strand: chain 'F' and resid 358 through 360 Processing sheet with id= AH, first strand: chain 'F' and resid 647 through 650 removed outlier: 6.666A pdb=" N ILE F 374 " --> pdb=" O ALA F 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR F 632 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS F 376 " --> pdb=" O THR F 632 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER F 553 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER F 377 " --> pdb=" O SER F 553 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS F 555 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR F 579 " --> pdb=" O GLY F 606 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 525 through 532 removed outlier: 3.937A pdb=" N GLU F 525 " --> pdb=" O ARG F 517 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG F 517 " --> pdb=" O GLU F 525 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL F 515 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE F 529 " --> pdb=" O LEU F 513 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU F 513 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG F 511 " --> pdb=" O PRO F 531 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU F 463 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL F 445 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 224 through 226 removed outlier: 3.566A pdb=" N ARG F 253 " --> pdb=" O GLN F 224 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP F 226 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL F 251 " --> pdb=" O ASP F 226 " (cutoff:3.500A) 1806 hydrogen bonds defined for protein. 5292 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: 14.42 Time building geometry restraints manager: 17.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9036 1.33 - 1.45: 8426 1.45 - 1.58: 21496 1.58 - 1.70: 0 1.70 - 1.83: 240 Bond restraints: 39198 Sorted by residual: bond pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP C1001 " pdb=" PA ADP C1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 ... (remaining 39193 not shown) Histogram of bond angle deviations from ideal: 88.39 - 97.52: 12 97.52 - 106.65: 1068 106.65 - 115.78: 24790 115.78 - 124.91: 26738 124.91 - 134.04: 648 Bond angle restraints: 53256 Sorted by residual: angle pdb=" O1A ADP C1001 " pdb=" PA ADP C1001 " pdb=" O5' ADP C1001 " ideal model delta sigma weight residual 108.20 88.39 19.81 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP F1001 " pdb=" PA ADP F1001 " pdb=" O5' ADP F1001 " ideal model delta sigma weight residual 108.20 88.39 19.81 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP D1001 " pdb=" PA ADP D1001 " pdb=" O5' ADP D1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP A1001 " pdb=" PA ADP A1001 " pdb=" O5' ADP A1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP E1001 " pdb=" PA ADP E1001 " pdb=" O5' ADP E1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 ... (remaining 53251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.30: 22464 30.30 - 60.60: 654 60.60 - 90.90: 24 90.90 - 121.20: 0 121.20 - 151.50: 12 Dihedral angle restraints: 23154 sinusoidal: 8988 harmonic: 14166 Sorted by residual: dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PA ADP D1001 " pdb=" PB ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PA ADP F1001 " pdb=" PB ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 23151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4111 0.038 - 0.076: 1586 0.076 - 0.114: 437 0.114 - 0.152: 76 0.152 - 0.190: 24 Chirality restraints: 6234 Sorted by residual: chirality pdb=" C2' ADP E1001 " pdb=" C1' ADP E1001 " pdb=" C3' ADP E1001 " pdb=" O2' ADP E1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" C2' ADP B1001 " pdb=" C1' ADP B1001 " pdb=" C3' ADP B1001 " pdb=" O2' ADP B1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" C2' ADP F1001 " pdb=" C1' ADP F1001 " pdb=" C3' ADP F1001 " pdb=" O2' ADP F1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 6231 not shown) Planarity restraints: 6708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 709 " -0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP D 709 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP D 709 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 709 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 709 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 709 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 709 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 709 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 709 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 709 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 709 " 0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP A 709 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 709 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 709 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 709 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 709 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 709 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 709 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 709 " -0.030 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP E 709 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP E 709 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 709 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 709 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 709 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 709 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 709 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 709 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 709 " -0.003 2.00e-02 2.50e+03 ... (remaining 6705 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 12808 2.84 - 3.42: 43624 3.42 - 3.99: 69686 3.99 - 4.57: 101120 4.57 - 5.14: 143886 Nonbonded interactions: 371124 Sorted by model distance: nonbonded pdb=" CB SER B 892 " pdb=" CD1 LEU C 902 " model vdw 2.268 3.860 nonbonded pdb=" CB SER E 892 " pdb=" CD1 LEU F 902 " model vdw 2.268 3.860 nonbonded pdb=" CB SER C 892 " pdb=" CD1 LEU D 902 " model vdw 2.268 3.860 nonbonded pdb=" CD1 LEU A 902 " pdb=" CB SER F 892 " model vdw 2.268 3.860 nonbonded pdb=" CB SER D 892 " pdb=" CD1 LEU E 902 " model vdw 2.268 3.860 ... (remaining 371119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 13.570 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 102.250 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 : 0.006 0.216 39198 Z= 0.396 Angle : 0.816 19.808 53256 Z= 0.391 Chirality : 0.044 0.190 6234 Planarity : 0.005 0.082 6708 Dihedral : 14.198 151.503 14070 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4938 helix: 0.88 (0.10), residues: 2544 sheet: -1.48 (0.28), residues: 318 loop : -2.07 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP D 709 HIS 0.007 0.001 HIS B 701 PHE 0.012 0.001 PHE C 841 TYR 0.016 0.002 TYR E 691 ARG 0.003 0.000 ARG E 859 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 983 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8122 (m-80) cc_final: 0.7825 (m-80) REVERT: A 252 LYS cc_start: 0.7080 (tptt) cc_final: 0.6764 (tptt) REVERT: A 303 PHE cc_start: 0.7289 (t80) cc_final: 0.6895 (t80) REVERT: A 317 ASN cc_start: 0.7889 (m-40) cc_final: 0.7683 (m-40) REVERT: A 385 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7632 (mtpp) REVERT: A 474 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7520 (ttpt) REVERT: A 567 GLU cc_start: 0.7319 (tp30) cc_final: 0.6822 (tp30) REVERT: A 569 SER cc_start: 0.8091 (m) cc_final: 0.7539 (p) REVERT: A 627 TYR cc_start: 0.8035 (m-80) cc_final: 0.7708 (m-80) REVERT: A 759 SER cc_start: 0.8300 (m) cc_final: 0.7897 (p) REVERT: A 844 TRP cc_start: 0.7956 (m-90) cc_final: 0.7697 (m-10) REVERT: A 898 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7641 (mmmm) REVERT: A 901 SER cc_start: 0.8341 (t) cc_final: 0.7590 (p) REVERT: A 904 ASP cc_start: 0.7485 (t0) cc_final: 0.7193 (t0) REVERT: A 910 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7562 (mt0) REVERT: B 171 GLU cc_start: 0.6783 (tp30) cc_final: 0.6549 (tp30) REVERT: B 317 ASN cc_start: 0.7905 (m-40) cc_final: 0.7674 (m-40) REVERT: B 332 ILE cc_start: 0.7821 (pt) cc_final: 0.7600 (pt) REVERT: B 369 LEU cc_start: 0.8190 (tp) cc_final: 0.7984 (tt) REVERT: B 385 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7754 (mtpp) REVERT: B 474 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7545 (ttpt) REVERT: B 498 TYR cc_start: 0.6825 (t80) cc_final: 0.6265 (t80) REVERT: B 539 ASP cc_start: 0.7029 (p0) cc_final: 0.6788 (p0) REVERT: B 548 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7332 (mtpp) REVERT: B 567 GLU cc_start: 0.7294 (tp30) cc_final: 0.6780 (tp30) REVERT: B 569 SER cc_start: 0.8150 (m) cc_final: 0.7913 (m) REVERT: B 582 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 627 TYR cc_start: 0.7886 (m-80) cc_final: 0.7638 (m-80) REVERT: B 656 ASP cc_start: 0.7293 (m-30) cc_final: 0.6890 (m-30) REVERT: B 749 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7968 (ptpt) REVERT: B 898 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7614 (mmmm) REVERT: B 901 SER cc_start: 0.8544 (t) cc_final: 0.8025 (p) REVERT: B 902 LEU cc_start: 0.8239 (tp) cc_final: 0.7940 (tp) REVERT: B 904 ASP cc_start: 0.7573 (t0) cc_final: 0.7278 (t0) REVERT: B 910 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7556 (mt0) REVERT: C 120 PHE cc_start: 0.7909 (m-80) cc_final: 0.7657 (m-80) REVERT: C 301 VAL cc_start: 0.8431 (t) cc_final: 0.7831 (m) REVERT: C 303 PHE cc_start: 0.7587 (t80) cc_final: 0.7258 (t80) REVERT: C 314 TYR cc_start: 0.7894 (m-80) cc_final: 0.7624 (m-80) REVERT: C 315 ARG cc_start: 0.7739 (mtt90) cc_final: 0.7525 (mtt90) REVERT: C 474 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7541 (ttpt) REVERT: C 481 LEU cc_start: 0.7293 (mm) cc_final: 0.7030 (mp) REVERT: C 539 ASP cc_start: 0.7034 (p0) cc_final: 0.6737 (p0) REVERT: C 548 LYS cc_start: 0.7777 (mtpp) cc_final: 0.7462 (mtpp) REVERT: C 569 SER cc_start: 0.8124 (m) cc_final: 0.7844 (m) REVERT: C 593 PRO cc_start: 0.8145 (Cg_exo) cc_final: 0.7914 (Cg_endo) REVERT: C 627 TYR cc_start: 0.7897 (m-80) cc_final: 0.7550 (m-80) REVERT: C 656 ASP cc_start: 0.7217 (m-30) cc_final: 0.6752 (m-30) REVERT: C 775 THR cc_start: 0.8344 (m) cc_final: 0.8142 (p) REVERT: C 844 TRP cc_start: 0.8079 (m-90) cc_final: 0.7841 (m-10) REVERT: C 865 PHE cc_start: 0.8160 (t80) cc_final: 0.7915 (t80) REVERT: C 898 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7538 (mmmm) REVERT: C 901 SER cc_start: 0.8483 (t) cc_final: 0.7990 (p) REVERT: C 904 ASP cc_start: 0.7563 (t0) cc_final: 0.7305 (t0) REVERT: C 910 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7491 (mt0) REVERT: D 303 PHE cc_start: 0.7503 (t80) cc_final: 0.7193 (t80) REVERT: D 385 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7569 (mtpp) REVERT: D 474 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7472 (ttpt) REVERT: D 481 LEU cc_start: 0.7206 (mm) cc_final: 0.6937 (mp) REVERT: D 498 TYR cc_start: 0.6990 (t80) cc_final: 0.6337 (t80) REVERT: D 539 ASP cc_start: 0.7188 (p0) cc_final: 0.6956 (p0) REVERT: D 566 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7143 (mtp85) REVERT: D 567 GLU cc_start: 0.7230 (tp30) cc_final: 0.6662 (tp30) REVERT: D 569 SER cc_start: 0.8102 (m) cc_final: 0.7551 (p) REVERT: D 582 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7328 (mm-30) REVERT: D 656 ASP cc_start: 0.7256 (m-30) cc_final: 0.6784 (m-30) REVERT: D 833 LEU cc_start: 0.8679 (tt) cc_final: 0.8471 (tp) REVERT: D 844 TRP cc_start: 0.8167 (m-90) cc_final: 0.7929 (m-10) REVERT: D 898 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7716 (mmmm) REVERT: D 901 SER cc_start: 0.8326 (t) cc_final: 0.7865 (p) REVERT: D 903 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6983 (mt-10) REVERT: D 904 ASP cc_start: 0.7520 (t0) cc_final: 0.7229 (t0) REVERT: D 910 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7632 (mt0) REVERT: E 164 GLN cc_start: 0.7008 (tt0) cc_final: 0.6776 (tt0) REVERT: E 171 GLU cc_start: 0.6962 (tp30) cc_final: 0.6670 (tp30) REVERT: E 176 LEU cc_start: 0.8360 (tp) cc_final: 0.7989 (tt) REVERT: E 300 LEU cc_start: 0.8437 (mt) cc_final: 0.8111 (mm) REVERT: E 303 PHE cc_start: 0.7468 (t80) cc_final: 0.7196 (t80) REVERT: E 312 SER cc_start: 0.8161 (m) cc_final: 0.7959 (p) REVERT: E 385 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7846 (mtpp) REVERT: E 474 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7006 (ttpt) REVERT: E 481 LEU cc_start: 0.7226 (mm) cc_final: 0.7013 (mp) REVERT: E 498 TYR cc_start: 0.6943 (t80) cc_final: 0.6379 (t80) REVERT: E 539 ASP cc_start: 0.7174 (p0) cc_final: 0.6959 (p0) REVERT: E 542 LYS cc_start: 0.7967 (pttp) cc_final: 0.7729 (pttp) REVERT: E 548 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7356 (mtpp) REVERT: E 570 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6904 (ttm170) REVERT: E 602 GLU cc_start: 0.6906 (tt0) cc_final: 0.6496 (tt0) REVERT: E 627 TYR cc_start: 0.7996 (m-80) cc_final: 0.7773 (m-80) REVERT: E 656 ASP cc_start: 0.7284 (m-30) cc_final: 0.6771 (m-30) REVERT: E 738 TYR cc_start: 0.6443 (m-80) cc_final: 0.6239 (m-80) REVERT: E 775 THR cc_start: 0.8322 (m) cc_final: 0.8081 (p) REVERT: E 898 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7645 (mmmm) REVERT: E 901 SER cc_start: 0.8397 (t) cc_final: 0.7928 (p) REVERT: E 902 LEU cc_start: 0.8152 (tp) cc_final: 0.7882 (tp) REVERT: E 904 ASP cc_start: 0.7476 (t0) cc_final: 0.7271 (t0) REVERT: F 164 GLN cc_start: 0.6901 (tt0) cc_final: 0.6669 (tt0) REVERT: F 252 LYS cc_start: 0.6937 (tptt) cc_final: 0.6570 (tptt) REVERT: F 301 VAL cc_start: 0.8416 (t) cc_final: 0.7813 (m) REVERT: F 303 PHE cc_start: 0.7503 (t80) cc_final: 0.7211 (t80) REVERT: F 359 ILE cc_start: 0.8150 (mp) cc_final: 0.7934 (mm) REVERT: F 361 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7550 (tp-100) REVERT: F 474 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7219 (ttpt) REVERT: F 569 SER cc_start: 0.8172 (m) cc_final: 0.7916 (m) REVERT: F 683 GLN cc_start: 0.7935 (mt0) cc_final: 0.7711 (mt0) REVERT: F 759 SER cc_start: 0.8103 (m) cc_final: 0.7801 (p) REVERT: F 775 THR cc_start: 0.8332 (m) cc_final: 0.8124 (p) REVERT: F 800 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7664 (tm-30) REVERT: F 806 ASN cc_start: 0.8140 (m-40) cc_final: 0.7939 (m-40) REVERT: F 833 LEU cc_start: 0.8560 (tt) cc_final: 0.8267 (tt) REVERT: F 844 TRP cc_start: 0.8104 (m-90) cc_final: 0.7848 (m-10) REVERT: F 898 LYS cc_start: 0.7985 (mmmm) cc_final: 0.7626 (mmmm) REVERT: F 901 SER cc_start: 0.8427 (t) cc_final: 0.7949 (p) REVERT: F 902 LEU cc_start: 0.7941 (tp) cc_final: 0.7739 (tt) outliers start: 0 outliers final: 0 residues processed: 983 average time/residue: 0.4889 time to fit residues: 784.4016 Evaluate side-chains 853 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 853 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 2.9990 chunk 372 optimal weight: 7.9990 chunk 206 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 251 optimal weight: 0.0770 chunk 199 optimal weight: 0.8980 chunk 385 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 446 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 815 ASN B 637 ASN B 683 GLN B 815 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN C 714 ASN D 164 GLN D 637 ASN D 683 GLN D 815 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 ASN E 637 ASN ** E 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 780 GLN E 815 ASN E 915 GLN F 637 ASN F 815 ASN F 915 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39198 Z= 0.207 Angle : 0.622 10.786 53256 Z= 0.309 Chirality : 0.042 0.156 6234 Planarity : 0.005 0.070 6708 Dihedral : 8.257 143.130 5328 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.37 % Favored : 92.51 % Rotamer: Outliers : 1.58 % Allowed : 9.33 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4938 helix: 1.20 (0.10), residues: 2526 sheet: -1.18 (0.28), residues: 324 loop : -2.24 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 709 HIS 0.007 0.001 HIS E 701 PHE 0.021 0.001 PHE C 600 TYR 0.025 0.002 TYR E 541 ARG 0.018 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 889 time to evaluate : 4.987 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 120 PHE cc_start: 0.8085 (m-80) cc_final: 0.7798 (m-80) REVERT: A 174 LYS cc_start: 0.7569 (tttp) cc_final: 0.7291 (tttp) REVERT: A 252 LYS cc_start: 0.7420 (tptt) cc_final: 0.6947 (tptt) REVERT: A 303 PHE cc_start: 0.7212 (t80) cc_final: 0.6858 (t80) REVERT: A 385 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7661 (mtpp) REVERT: A 474 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7700 (ttpt) REVERT: A 567 GLU cc_start: 0.7218 (tp30) cc_final: 0.6769 (tp30) REVERT: A 569 SER cc_start: 0.8105 (m) cc_final: 0.7604 (p) REVERT: A 595 SER cc_start: 0.8459 (p) cc_final: 0.7916 (t) REVERT: A 596 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: A 605 ASP cc_start: 0.6923 (m-30) cc_final: 0.6722 (m-30) REVERT: A 720 GLU cc_start: 0.7205 (mp0) cc_final: 0.6934 (mp0) REVERT: A 759 SER cc_start: 0.8306 (m) cc_final: 0.7891 (p) REVERT: A 809 ILE cc_start: 0.8333 (tp) cc_final: 0.8125 (tt) REVERT: A 844 TRP cc_start: 0.8071 (m-90) cc_final: 0.7818 (m-10) REVERT: A 898 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7659 (mmmm) REVERT: A 901 SER cc_start: 0.8443 (t) cc_final: 0.7708 (p) REVERT: A 904 ASP cc_start: 0.7568 (t0) cc_final: 0.7278 (t0) REVERT: A 905 PHE cc_start: 0.8232 (t80) cc_final: 0.7960 (t80) REVERT: A 911 ARG cc_start: 0.7502 (mtt180) cc_final: 0.7286 (mtt180) REVERT: B 116 PHE cc_start: 0.7702 (t80) cc_final: 0.7460 (t80) REVERT: B 120 PHE cc_start: 0.8225 (m-80) cc_final: 0.7770 (m-80) REVERT: B 171 GLU cc_start: 0.6672 (tp30) cc_final: 0.6337 (tp30) REVERT: B 174 LYS cc_start: 0.7638 (tttp) cc_final: 0.7411 (tttp) REVERT: B 346 MET cc_start: 0.7659 (mmp) cc_final: 0.7438 (mmp) REVERT: B 385 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7711 (mtpp) REVERT: B 474 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7754 (ttpt) REVERT: B 539 ASP cc_start: 0.6995 (p0) cc_final: 0.6713 (p0) REVERT: B 558 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7112 (m) REVERT: B 567 GLU cc_start: 0.7198 (tp30) cc_final: 0.6693 (tp30) REVERT: B 569 SER cc_start: 0.8068 (m) cc_final: 0.7824 (m) REVERT: B 599 ASP cc_start: 0.7724 (t0) cc_final: 0.7381 (t0) REVERT: B 656 ASP cc_start: 0.7325 (m-30) cc_final: 0.6913 (m-30) REVERT: B 844 TRP cc_start: 0.8198 (m-90) cc_final: 0.7867 (m-10) REVERT: B 898 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7720 (mmmm) REVERT: B 904 ASP cc_start: 0.7584 (t0) cc_final: 0.7268 (t0) REVERT: C 120 PHE cc_start: 0.7902 (m-80) cc_final: 0.7642 (m-80) REVERT: C 171 GLU cc_start: 0.6927 (tp30) cc_final: 0.6482 (tp30) REVERT: C 174 LYS cc_start: 0.7529 (tttp) cc_final: 0.7322 (tttp) REVERT: C 303 PHE cc_start: 0.7461 (t80) cc_final: 0.7245 (t80) REVERT: C 314 TYR cc_start: 0.7887 (m-80) cc_final: 0.7485 (m-80) REVERT: C 380 THR cc_start: 0.8036 (t) cc_final: 0.7666 (p) REVERT: C 403 ASP cc_start: 0.5265 (t70) cc_final: 0.4992 (t0) REVERT: C 474 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7603 (ttpt) REVERT: C 539 ASP cc_start: 0.6939 (p0) cc_final: 0.6659 (p0) REVERT: C 542 LYS cc_start: 0.7942 (pttp) cc_final: 0.7740 (pttp) REVERT: C 567 GLU cc_start: 0.7168 (tp30) cc_final: 0.6704 (tp30) REVERT: C 569 SER cc_start: 0.8198 (m) cc_final: 0.7906 (m) REVERT: C 627 TYR cc_start: 0.7856 (m-80) cc_final: 0.7558 (m-80) REVERT: C 656 ASP cc_start: 0.7151 (m-30) cc_final: 0.6833 (m-30) REVERT: C 844 TRP cc_start: 0.8097 (m-90) cc_final: 0.7889 (m-10) REVERT: C 865 PHE cc_start: 0.8124 (t80) cc_final: 0.7846 (t80) REVERT: C 898 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7517 (mmmm) REVERT: C 901 SER cc_start: 0.8488 (t) cc_final: 0.7959 (p) REVERT: C 904 ASP cc_start: 0.7581 (t0) cc_final: 0.7267 (t0) REVERT: C 910 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7468 (mt0) REVERT: D 171 GLU cc_start: 0.7022 (tp30) cc_final: 0.6585 (tp30) REVERT: D 174 LYS cc_start: 0.7539 (tttp) cc_final: 0.7277 (tttp) REVERT: D 209 ILE cc_start: 0.8185 (mm) cc_final: 0.7878 (tp) REVERT: D 303 PHE cc_start: 0.7427 (t80) cc_final: 0.7144 (t80) REVERT: D 385 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7644 (mtpp) REVERT: D 474 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7573 (ttpt) REVERT: D 481 LEU cc_start: 0.7275 (mm) cc_final: 0.7061 (mp) REVERT: D 539 ASP cc_start: 0.7072 (p0) cc_final: 0.6826 (p0) REVERT: D 567 GLU cc_start: 0.7130 (tp30) cc_final: 0.6653 (tp30) REVERT: D 569 SER cc_start: 0.8147 (m) cc_final: 0.7626 (p) REVERT: D 582 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 605 ASP cc_start: 0.6876 (m-30) cc_final: 0.6667 (m-30) REVERT: D 627 TYR cc_start: 0.7974 (m-80) cc_final: 0.7681 (m-80) REVERT: D 656 ASP cc_start: 0.7130 (m-30) cc_final: 0.6690 (m-30) REVERT: D 679 LYS cc_start: 0.8282 (mtmm) cc_final: 0.8020 (mtpp) REVERT: D 759 SER cc_start: 0.8235 (m) cc_final: 0.7875 (p) REVERT: D 833 LEU cc_start: 0.8558 (tt) cc_final: 0.8281 (tp) REVERT: D 844 TRP cc_start: 0.8140 (m-90) cc_final: 0.7927 (m-10) REVERT: D 898 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7709 (mmmm) REVERT: D 901 SER cc_start: 0.8434 (t) cc_final: 0.7974 (p) REVERT: D 903 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6959 (mt-10) REVERT: D 904 ASP cc_start: 0.7621 (t0) cc_final: 0.7290 (t0) REVERT: E 171 GLU cc_start: 0.6866 (tp30) cc_final: 0.6519 (tp30) REVERT: E 300 LEU cc_start: 0.8379 (mt) cc_final: 0.8111 (mm) REVERT: E 312 SER cc_start: 0.8053 (m) cc_final: 0.7730 (p) REVERT: E 317 ASN cc_start: 0.8088 (m110) cc_final: 0.7836 (m110) REVERT: E 355 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7827 (ttmt) REVERT: E 357 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7640 (mmmm) REVERT: E 481 LEU cc_start: 0.7281 (mm) cc_final: 0.7045 (mp) REVERT: E 498 TYR cc_start: 0.6853 (t80) cc_final: 0.6435 (t80) REVERT: E 539 ASP cc_start: 0.7065 (p0) cc_final: 0.6818 (p0) REVERT: E 569 SER cc_start: 0.8168 (m) cc_final: 0.7904 (m) REVERT: E 595 SER cc_start: 0.8424 (p) cc_final: 0.8192 (p) REVERT: E 627 TYR cc_start: 0.7941 (m-80) cc_final: 0.7721 (m-80) REVERT: E 656 ASP cc_start: 0.7233 (m-30) cc_final: 0.6949 (m-30) REVERT: E 667 LEU cc_start: 0.8410 (mt) cc_final: 0.7636 (mt) REVERT: E 898 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7635 (mmmm) REVERT: E 901 SER cc_start: 0.8348 (t) cc_final: 0.7863 (p) REVERT: E 904 ASP cc_start: 0.7542 (t0) cc_final: 0.7282 (t0) REVERT: F 120 PHE cc_start: 0.7931 (m-80) cc_final: 0.7730 (m-10) REVERT: F 209 ILE cc_start: 0.8170 (mm) cc_final: 0.7801 (tp) REVERT: F 252 LYS cc_start: 0.7059 (tptt) cc_final: 0.6648 (tptt) REVERT: F 385 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7906 (mtpp) REVERT: F 474 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7248 (ttpt) REVERT: F 567 GLU cc_start: 0.7193 (tp30) cc_final: 0.6718 (tp30) REVERT: F 569 SER cc_start: 0.8196 (m) cc_final: 0.7684 (p) REVERT: F 695 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7554 (tpt170) REVERT: F 833 LEU cc_start: 0.8459 (tt) cc_final: 0.8182 (tt) REVERT: F 844 TRP cc_start: 0.8223 (m-90) cc_final: 0.7893 (m-10) REVERT: F 898 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7615 (mmmm) REVERT: F 901 SER cc_start: 0.8343 (t) cc_final: 0.7960 (p) REVERT: F 910 GLN cc_start: 0.7890 (mt0) cc_final: 0.7625 (mt0) outliers start: 65 outliers final: 46 residues processed: 897 average time/residue: 0.5102 time to fit residues: 746.0335 Evaluate side-chains 901 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 853 time to evaluate : 4.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 864 SER Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 371 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 447 optimal weight: 9.9990 chunk 483 optimal weight: 0.9990 chunk 398 optimal weight: 0.7980 chunk 443 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 359 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 806 ASN A 815 ASN B 291 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN C 637 ASN C 806 ASN D 164 GLN D 637 ASN D 683 GLN E 637 ASN E 815 ASN F 637 ASN F 806 ASN F 815 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39198 Z= 0.202 Angle : 0.583 7.580 53256 Z= 0.289 Chirality : 0.042 0.162 6234 Planarity : 0.004 0.058 6708 Dihedral : 7.844 137.238 5328 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.02 % Allowed : 12.60 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4938 helix: 1.38 (0.10), residues: 2538 sheet: -1.17 (0.28), residues: 324 loop : -2.22 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 709 HIS 0.007 0.001 HIS E 701 PHE 0.014 0.001 PHE B 868 TYR 0.023 0.002 TYR A 541 ARG 0.006 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 900 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8126 (m-80) cc_final: 0.7758 (m-80) REVERT: A 202 LEU cc_start: 0.6739 (mt) cc_final: 0.6528 (mp) REVERT: A 357 LYS cc_start: 0.7943 (mmtp) cc_final: 0.7719 (UNCLASSIFIED) REVERT: A 385 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7702 (mtpp) REVERT: A 474 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7753 (ttpt) REVERT: A 558 THR cc_start: 0.8022 (m) cc_final: 0.7736 (t) REVERT: A 567 GLU cc_start: 0.7142 (tp30) cc_final: 0.6764 (tp30) REVERT: A 569 SER cc_start: 0.8113 (m) cc_final: 0.7626 (p) REVERT: A 599 ASP cc_start: 0.7718 (m-30) cc_final: 0.7473 (m-30) REVERT: A 617 ASN cc_start: 0.8224 (m-40) cc_final: 0.7984 (m110) REVERT: A 624 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7608 (mt0) REVERT: A 654 SER cc_start: 0.8607 (p) cc_final: 0.8271 (p) REVERT: A 667 LEU cc_start: 0.8514 (mt) cc_final: 0.8187 (mt) REVERT: A 759 SER cc_start: 0.8211 (m) cc_final: 0.7836 (p) REVERT: A 844 TRP cc_start: 0.8178 (m-90) cc_final: 0.7908 (m-10) REVERT: A 898 LYS cc_start: 0.8045 (mmmm) cc_final: 0.7590 (mmmm) REVERT: A 901 SER cc_start: 0.8437 (t) cc_final: 0.7710 (p) REVERT: A 904 ASP cc_start: 0.7531 (t0) cc_final: 0.7190 (t0) REVERT: A 905 PHE cc_start: 0.8259 (t80) cc_final: 0.7966 (t80) REVERT: B 116 PHE cc_start: 0.7695 (t80) cc_final: 0.7458 (t80) REVERT: B 120 PHE cc_start: 0.8198 (m-80) cc_final: 0.7758 (m-80) REVERT: B 171 GLU cc_start: 0.6730 (tp30) cc_final: 0.6447 (tp30) REVERT: B 174 LYS cc_start: 0.7690 (tttp) cc_final: 0.7465 (tttp) REVERT: B 224 GLN cc_start: 0.6693 (mp10) cc_final: 0.6428 (mp10) REVERT: B 346 MET cc_start: 0.7611 (mmp) cc_final: 0.7373 (mmp) REVERT: B 385 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7762 (mtpp) REVERT: B 387 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7357 (pttm) REVERT: B 474 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7780 (ttpt) REVERT: B 498 TYR cc_start: 0.6694 (t80) cc_final: 0.6387 (t80) REVERT: B 539 ASP cc_start: 0.6999 (p0) cc_final: 0.6708 (p0) REVERT: B 567 GLU cc_start: 0.7146 (tp30) cc_final: 0.6690 (tp30) REVERT: B 569 SER cc_start: 0.8135 (m) cc_final: 0.7915 (m) REVERT: B 582 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7161 (mm-30) REVERT: B 624 GLN cc_start: 0.7904 (mm110) cc_final: 0.7633 (mt0) REVERT: B 625 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7647 (mmt-90) REVERT: B 656 ASP cc_start: 0.7331 (m-30) cc_final: 0.6997 (m-30) REVERT: B 844 TRP cc_start: 0.8295 (m-90) cc_final: 0.7916 (m-10) REVERT: B 848 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6849 (mm-30) REVERT: B 898 LYS cc_start: 0.7938 (mmmm) cc_final: 0.7626 (mmmm) REVERT: B 904 ASP cc_start: 0.7620 (t0) cc_final: 0.7290 (t0) REVERT: B 911 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7546 (mtt180) REVERT: C 120 PHE cc_start: 0.7851 (m-80) cc_final: 0.7555 (m-80) REVERT: C 171 GLU cc_start: 0.6936 (tp30) cc_final: 0.6543 (tp30) REVERT: C 174 LYS cc_start: 0.7586 (tttp) cc_final: 0.7331 (tttp) REVERT: C 303 PHE cc_start: 0.7433 (t80) cc_final: 0.7204 (t80) REVERT: C 314 TYR cc_start: 0.7899 (m-80) cc_final: 0.7642 (m-80) REVERT: C 361 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7661 (tp-100) REVERT: C 380 THR cc_start: 0.8105 (t) cc_final: 0.7717 (p) REVERT: C 423 ASP cc_start: 0.7872 (t70) cc_final: 0.7559 (t70) REVERT: C 474 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7638 (ttpt) REVERT: C 539 ASP cc_start: 0.6978 (p0) cc_final: 0.6687 (p0) REVERT: C 567 GLU cc_start: 0.6994 (tp30) cc_final: 0.6746 (tp30) REVERT: C 569 SER cc_start: 0.8236 (m) cc_final: 0.7927 (m) REVERT: C 627 TYR cc_start: 0.7828 (m-80) cc_final: 0.7563 (m-80) REVERT: C 656 ASP cc_start: 0.7172 (m-30) cc_final: 0.6838 (m-30) REVERT: C 844 TRP cc_start: 0.8131 (m-90) cc_final: 0.7890 (m-10) REVERT: C 865 PHE cc_start: 0.8092 (t80) cc_final: 0.7821 (t80) REVERT: C 898 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7507 (mmmm) REVERT: C 901 SER cc_start: 0.8462 (t) cc_final: 0.7940 (p) REVERT: C 904 ASP cc_start: 0.7567 (t0) cc_final: 0.7254 (t0) REVERT: D 171 GLU cc_start: 0.6990 (tp30) cc_final: 0.6587 (tp30) REVERT: D 174 LYS cc_start: 0.7643 (tttp) cc_final: 0.7418 (tttp) REVERT: D 303 PHE cc_start: 0.7414 (t80) cc_final: 0.7120 (t80) REVERT: D 474 LYS cc_start: 0.8039 (ttpt) cc_final: 0.7617 (ttpt) REVERT: D 498 TYR cc_start: 0.6817 (t80) cc_final: 0.6450 (t80) REVERT: D 539 ASP cc_start: 0.7074 (p0) cc_final: 0.6845 (p0) REVERT: D 548 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7420 (mtpp) REVERT: D 567 GLU cc_start: 0.7061 (tp30) cc_final: 0.6652 (tp30) REVERT: D 569 SER cc_start: 0.8141 (m) cc_final: 0.7626 (p) REVERT: D 582 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 627 TYR cc_start: 0.7883 (m-80) cc_final: 0.7666 (m-80) REVERT: D 656 ASP cc_start: 0.7108 (m-30) cc_final: 0.6697 (m-30) REVERT: D 730 ASP cc_start: 0.6998 (t0) cc_final: 0.6685 (t0) REVERT: D 833 LEU cc_start: 0.8438 (tt) cc_final: 0.8188 (tp) REVERT: D 898 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7721 (mmmm) REVERT: D 901 SER cc_start: 0.8416 (t) cc_final: 0.7937 (p) REVERT: D 904 ASP cc_start: 0.7581 (t0) cc_final: 0.7239 (t0) REVERT: E 171 GLU cc_start: 0.6949 (tp30) cc_final: 0.6650 (tp30) REVERT: E 252 LYS cc_start: 0.7153 (tptt) cc_final: 0.6821 (tptt) REVERT: E 300 LEU cc_start: 0.8340 (mt) cc_final: 0.8083 (mm) REVERT: E 346 MET cc_start: 0.7539 (mmm) cc_final: 0.7304 (mmm) REVERT: E 355 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7843 (ttmt) REVERT: E 498 TYR cc_start: 0.6771 (t80) cc_final: 0.6508 (t80) REVERT: E 537 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7767 (mtt90) REVERT: E 539 ASP cc_start: 0.7131 (p0) cc_final: 0.6884 (p0) REVERT: E 569 SER cc_start: 0.8100 (m) cc_final: 0.7830 (m) REVERT: E 582 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7015 (mm-30) REVERT: E 599 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: E 638 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6603 (p0) REVERT: E 656 ASP cc_start: 0.7349 (m-30) cc_final: 0.6902 (m-30) REVERT: E 667 LEU cc_start: 0.8396 (mt) cc_final: 0.7733 (mt) REVERT: E 783 ASN cc_start: 0.8563 (p0) cc_final: 0.8196 (p0) REVERT: E 848 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6873 (mm-30) REVERT: E 878 LEU cc_start: 0.8178 (mp) cc_final: 0.7870 (mp) REVERT: E 898 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7603 (mmmm) REVERT: E 901 SER cc_start: 0.8414 (t) cc_final: 0.7914 (p) REVERT: E 904 ASP cc_start: 0.7490 (t0) cc_final: 0.7230 (t0) REVERT: F 120 PHE cc_start: 0.7916 (m-80) cc_final: 0.7682 (m-10) REVERT: F 171 GLU cc_start: 0.6809 (tp30) cc_final: 0.6469 (tp30) REVERT: F 174 LYS cc_start: 0.7412 (tttp) cc_final: 0.7171 (tttp) REVERT: F 209 ILE cc_start: 0.8235 (mm) cc_final: 0.7854 (tp) REVERT: F 252 LYS cc_start: 0.7251 (tptt) cc_final: 0.6750 (tptt) REVERT: F 385 LYS cc_start: 0.8217 (mtpp) cc_final: 0.8009 (mtpp) REVERT: F 474 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7355 (ttpt) REVERT: F 501 LYS cc_start: 0.7369 (tptt) cc_final: 0.7151 (tppt) REVERT: F 505 PHE cc_start: 0.7801 (m-10) cc_final: 0.7594 (m-80) REVERT: F 567 GLU cc_start: 0.7149 (tp30) cc_final: 0.6745 (tp30) REVERT: F 569 SER cc_start: 0.8252 (m) cc_final: 0.7734 (p) REVERT: F 695 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7631 (tpt90) REVERT: F 833 LEU cc_start: 0.8334 (tt) cc_final: 0.8122 (tt) REVERT: F 844 TRP cc_start: 0.8370 (m-90) cc_final: 0.7970 (m-10) REVERT: F 898 LYS cc_start: 0.8010 (mmmm) cc_final: 0.7618 (mmmm) REVERT: F 901 SER cc_start: 0.8433 (t) cc_final: 0.7946 (p) REVERT: F 910 GLN cc_start: 0.7813 (mt0) cc_final: 0.7575 (mt0) outliers start: 83 outliers final: 47 residues processed: 919 average time/residue: 0.4920 time to fit residues: 733.9250 Evaluate side-chains 888 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 837 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 599 ASP Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 0.9980 chunk 336 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 449 optimal weight: 8.9990 chunk 475 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 425 optimal weight: 10.0000 chunk 128 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 815 ASN A 910 GLN B 291 ASN B 317 ASN B 637 ASN B 815 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN C 571 GLN C 637 ASN C 780 GLN C 806 ASN C 916 HIS E 291 ASN E 637 ASN E 815 ASN F 815 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39198 Z= 0.186 Angle : 0.568 7.279 53256 Z= 0.280 Chirality : 0.041 0.151 6234 Planarity : 0.004 0.064 6708 Dihedral : 7.550 128.634 5328 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.14 % Allowed : 15.08 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 4938 helix: 1.49 (0.11), residues: 2538 sheet: -1.17 (0.28), residues: 324 loop : -2.15 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 846 HIS 0.006 0.001 HIS E 701 PHE 0.014 0.001 PHE B 868 TYR 0.021 0.001 TYR C 616 ARG 0.006 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 887 time to evaluate : 4.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8104 (m-80) cc_final: 0.7775 (m-80) REVERT: A 124 ILE cc_start: 0.7364 (tt) cc_final: 0.7122 (tt) REVERT: A 171 GLU cc_start: 0.6849 (tp30) cc_final: 0.6466 (tp30) REVERT: A 174 LYS cc_start: 0.7674 (tttp) cc_final: 0.7453 (tttp) REVERT: A 202 LEU cc_start: 0.6820 (mt) cc_final: 0.6618 (mp) REVERT: A 224 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: A 385 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7732 (mtpp) REVERT: A 474 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7725 (ttpt) REVERT: A 558 THR cc_start: 0.8076 (m) cc_final: 0.7809 (t) REVERT: A 567 GLU cc_start: 0.7142 (tp30) cc_final: 0.6772 (tp30) REVERT: A 569 SER cc_start: 0.8143 (m) cc_final: 0.7658 (p) REVERT: A 599 ASP cc_start: 0.7702 (m-30) cc_final: 0.7460 (m-30) REVERT: A 605 ASP cc_start: 0.6861 (m-30) cc_final: 0.6574 (t0) REVERT: A 617 ASN cc_start: 0.8214 (m-40) cc_final: 0.7992 (m110) REVERT: A 624 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7616 (mt0) REVERT: A 627 TYR cc_start: 0.7894 (m-80) cc_final: 0.7677 (m-80) REVERT: A 746 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7632 (t) REVERT: A 759 SER cc_start: 0.8155 (m) cc_final: 0.7824 (p) REVERT: A 844 TRP cc_start: 0.8204 (m-90) cc_final: 0.7886 (m-10) REVERT: A 848 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6663 (mm-30) REVERT: A 898 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7537 (mmmm) REVERT: A 901 SER cc_start: 0.8434 (t) cc_final: 0.7710 (p) REVERT: A 904 ASP cc_start: 0.7551 (t0) cc_final: 0.7213 (t0) REVERT: B 116 PHE cc_start: 0.7706 (t80) cc_final: 0.7464 (t80) REVERT: B 120 PHE cc_start: 0.8191 (m-80) cc_final: 0.7773 (m-80) REVERT: B 171 GLU cc_start: 0.6833 (tp30) cc_final: 0.6576 (tp30) REVERT: B 174 LYS cc_start: 0.7720 (tttp) cc_final: 0.7482 (tttp) REVERT: B 385 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7893 (mtpp) REVERT: B 387 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7509 (pttm) REVERT: B 474 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7709 (ttpt) REVERT: B 498 TYR cc_start: 0.6704 (t80) cc_final: 0.6399 (t80) REVERT: B 539 ASP cc_start: 0.7007 (p0) cc_final: 0.6731 (p0) REVERT: B 567 GLU cc_start: 0.7125 (tp30) cc_final: 0.6702 (tp30) REVERT: B 569 SER cc_start: 0.8146 (m) cc_final: 0.7915 (m) REVERT: B 582 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7116 (mm-30) REVERT: B 599 ASP cc_start: 0.7723 (t0) cc_final: 0.7297 (t0) REVERT: B 617 ASN cc_start: 0.8063 (m-40) cc_final: 0.7836 (m-40) REVERT: B 624 GLN cc_start: 0.7919 (mm110) cc_final: 0.7661 (mt0) REVERT: B 625 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7737 (mmt-90) REVERT: B 627 TYR cc_start: 0.7746 (m-80) cc_final: 0.7469 (m-10) REVERT: B 656 ASP cc_start: 0.7386 (m-30) cc_final: 0.6975 (m-30) REVERT: B 844 TRP cc_start: 0.8303 (m-90) cc_final: 0.7929 (m-10) REVERT: B 848 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6909 (mm-30) REVERT: B 898 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7624 (mmmm) REVERT: B 904 ASP cc_start: 0.7600 (t0) cc_final: 0.7278 (t0) REVERT: B 911 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7596 (mtt180) REVERT: C 120 PHE cc_start: 0.7840 (m-80) cc_final: 0.7512 (m-80) REVERT: C 171 GLU cc_start: 0.6913 (tp30) cc_final: 0.6578 (tp30) REVERT: C 303 PHE cc_start: 0.7420 (t80) cc_final: 0.7190 (t80) REVERT: C 314 TYR cc_start: 0.7916 (m-80) cc_final: 0.7644 (m-80) REVERT: C 380 THR cc_start: 0.8154 (t) cc_final: 0.7720 (p) REVERT: C 423 ASP cc_start: 0.7862 (t70) cc_final: 0.7525 (t70) REVERT: C 474 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7775 (ttpt) REVERT: C 539 ASP cc_start: 0.6913 (p0) cc_final: 0.6618 (p0) REVERT: C 569 SER cc_start: 0.8195 (m) cc_final: 0.7706 (p) REVERT: C 627 TYR cc_start: 0.7826 (m-80) cc_final: 0.7580 (m-80) REVERT: C 643 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8142 (mtpp) REVERT: C 656 ASP cc_start: 0.7149 (m-30) cc_final: 0.6733 (m-30) REVERT: C 759 SER cc_start: 0.7989 (m) cc_final: 0.7704 (p) REVERT: C 844 TRP cc_start: 0.8123 (m-90) cc_final: 0.7894 (m-10) REVERT: C 865 PHE cc_start: 0.8095 (t80) cc_final: 0.7832 (t80) REVERT: C 898 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7495 (mmmm) REVERT: C 901 SER cc_start: 0.8473 (t) cc_final: 0.7935 (p) REVERT: C 904 ASP cc_start: 0.7545 (t0) cc_final: 0.7247 (t0) REVERT: D 171 GLU cc_start: 0.6970 (tp30) cc_final: 0.6649 (tp30) REVERT: D 174 LYS cc_start: 0.7657 (tttp) cc_final: 0.7420 (tttp) REVERT: D 303 PHE cc_start: 0.7389 (t80) cc_final: 0.7082 (t80) REVERT: D 474 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7582 (ttpt) REVERT: D 498 TYR cc_start: 0.6810 (t80) cc_final: 0.6473 (t80) REVERT: D 539 ASP cc_start: 0.7096 (p0) cc_final: 0.6833 (p0) REVERT: D 548 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7474 (mtpp) REVERT: D 567 GLU cc_start: 0.7059 (tp30) cc_final: 0.6669 (tp30) REVERT: D 569 SER cc_start: 0.8206 (m) cc_final: 0.7704 (p) REVERT: D 582 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7209 (mm-30) REVERT: D 595 SER cc_start: 0.8674 (p) cc_final: 0.8265 (p) REVERT: D 599 ASP cc_start: 0.7753 (m-30) cc_final: 0.7479 (m-30) REVERT: D 605 ASP cc_start: 0.6808 (m-30) cc_final: 0.6576 (t0) REVERT: D 615 LYS cc_start: 0.8423 (mtpp) cc_final: 0.7704 (mtmt) REVERT: D 627 TYR cc_start: 0.7772 (m-80) cc_final: 0.7545 (m-80) REVERT: D 656 ASP cc_start: 0.7101 (m-30) cc_final: 0.6798 (m-30) REVERT: D 679 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7971 (mtpp) REVERT: D 730 ASP cc_start: 0.6970 (t0) cc_final: 0.6690 (t0) REVERT: D 833 LEU cc_start: 0.8352 (tt) cc_final: 0.8116 (tp) REVERT: D 848 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6906 (mm-30) REVERT: D 898 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7794 (mmmm) REVERT: D 904 ASP cc_start: 0.7597 (t0) cc_final: 0.7238 (t0) REVERT: D 917 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7170 (tm-30) REVERT: E 171 GLU cc_start: 0.7020 (tp30) cc_final: 0.6729 (tp30) REVERT: E 252 LYS cc_start: 0.7163 (tptt) cc_final: 0.6804 (tptt) REVERT: E 355 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7870 (ttmt) REVERT: E 357 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7657 (mmmm) REVERT: E 498 TYR cc_start: 0.6811 (t80) cc_final: 0.6532 (t80) REVERT: E 539 ASP cc_start: 0.7106 (p0) cc_final: 0.6861 (p0) REVERT: E 558 THR cc_start: 0.7958 (m) cc_final: 0.7693 (t) REVERT: E 569 SER cc_start: 0.8153 (m) cc_final: 0.7882 (m) REVERT: E 582 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6945 (mm-30) REVERT: E 599 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: E 624 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7716 (mt0) REVERT: E 656 ASP cc_start: 0.7301 (m-30) cc_final: 0.6917 (m-30) REVERT: E 667 LEU cc_start: 0.8112 (mt) cc_final: 0.7678 (mp) REVERT: E 783 ASN cc_start: 0.8602 (p0) cc_final: 0.8287 (p0) REVERT: E 843 ILE cc_start: 0.8800 (mm) cc_final: 0.8476 (mt) REVERT: E 848 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6907 (mm-30) REVERT: E 878 LEU cc_start: 0.8090 (mp) cc_final: 0.7811 (mp) REVERT: E 898 LYS cc_start: 0.7928 (mmmm) cc_final: 0.7555 (mmmm) REVERT: E 901 SER cc_start: 0.8416 (t) cc_final: 0.7902 (p) REVERT: E 904 ASP cc_start: 0.7462 (t0) cc_final: 0.7182 (t0) REVERT: F 120 PHE cc_start: 0.7931 (m-80) cc_final: 0.7664 (m-10) REVERT: F 171 GLU cc_start: 0.6791 (tp30) cc_final: 0.6481 (tp30) REVERT: F 252 LYS cc_start: 0.7293 (tptt) cc_final: 0.6780 (tptt) REVERT: F 385 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7841 (mtpp) REVERT: F 387 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7540 (pttm) REVERT: F 474 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7457 (ttpt) REVERT: F 501 LYS cc_start: 0.7382 (tptt) cc_final: 0.7066 (tppt) REVERT: F 504 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7443 (tm-30) REVERT: F 567 GLU cc_start: 0.7123 (tp30) cc_final: 0.6767 (tp30) REVERT: F 569 SER cc_start: 0.8221 (m) cc_final: 0.7720 (p) REVERT: F 833 LEU cc_start: 0.8265 (tt) cc_final: 0.8057 (tt) REVERT: F 844 TRP cc_start: 0.8370 (m-90) cc_final: 0.7972 (m-10) REVERT: F 865 PHE cc_start: 0.8222 (t80) cc_final: 0.7908 (t80) REVERT: F 898 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7574 (mmmm) REVERT: F 901 SER cc_start: 0.8471 (t) cc_final: 0.7976 (p) REVERT: F 904 ASP cc_start: 0.7396 (t0) cc_final: 0.7087 (t0) REVERT: F 910 GLN cc_start: 0.7862 (mt0) cc_final: 0.7613 (mt0) outliers start: 88 outliers final: 53 residues processed: 909 average time/residue: 0.5275 time to fit residues: 784.1194 Evaluate side-chains 908 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 849 time to evaluate : 4.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 599 ASP Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 850 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 0.6980 chunk 269 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 354 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 405 optimal weight: 0.9990 chunk 328 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 242 optimal weight: 0.9990 chunk 426 optimal weight: 0.4980 chunk 120 optimal weight: 20.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 815 ASN A 910 GLN B 637 ASN B 683 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 806 ASN D 910 GLN E 637 ASN E 714 ASN E 815 ASN F 815 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39198 Z= 0.190 Angle : 0.561 11.958 53256 Z= 0.275 Chirality : 0.041 0.144 6234 Planarity : 0.004 0.057 6708 Dihedral : 7.305 123.030 5328 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.80 % Allowed : 16.01 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4938 helix: 1.55 (0.10), residues: 2538 sheet: -1.17 (0.29), residues: 324 loop : -2.14 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 846 HIS 0.007 0.001 HIS E 701 PHE 0.014 0.001 PHE B 868 TYR 0.021 0.001 TYR C 616 ARG 0.004 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 878 time to evaluate : 4.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8070 (m-80) cc_final: 0.7707 (m-80) REVERT: A 171 GLU cc_start: 0.6842 (tp30) cc_final: 0.6457 (tp30) REVERT: A 174 LYS cc_start: 0.7709 (tttp) cc_final: 0.7479 (tttp) REVERT: A 357 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7698 (mmmm) REVERT: A 385 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7714 (mtpp) REVERT: A 387 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7559 (pttm) REVERT: A 474 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7740 (ttpt) REVERT: A 505 PHE cc_start: 0.7655 (m-10) cc_final: 0.7428 (m-10) REVERT: A 541 TYR cc_start: 0.7333 (t80) cc_final: 0.7094 (t80) REVERT: A 558 THR cc_start: 0.8128 (m) cc_final: 0.7912 (t) REVERT: A 567 GLU cc_start: 0.7112 (tp30) cc_final: 0.6779 (tp30) REVERT: A 569 SER cc_start: 0.8144 (m) cc_final: 0.7652 (p) REVERT: A 599 ASP cc_start: 0.7679 (m-30) cc_final: 0.7441 (m-30) REVERT: A 617 ASN cc_start: 0.8221 (m-40) cc_final: 0.7999 (m-40) REVERT: A 624 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7622 (mt0) REVERT: A 746 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7600 (t) REVERT: A 759 SER cc_start: 0.8165 (m) cc_final: 0.7772 (p) REVERT: A 844 TRP cc_start: 0.8242 (m-90) cc_final: 0.7853 (m-10) REVERT: A 848 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6660 (mm-30) REVERT: A 898 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7493 (mmmm) REVERT: A 901 SER cc_start: 0.8426 (t) cc_final: 0.7730 (p) REVERT: A 904 ASP cc_start: 0.7561 (t0) cc_final: 0.7236 (t0) REVERT: B 116 PHE cc_start: 0.7696 (t80) cc_final: 0.7448 (t80) REVERT: B 120 PHE cc_start: 0.8180 (m-80) cc_final: 0.7773 (m-80) REVERT: B 171 GLU cc_start: 0.6856 (tp30) cc_final: 0.6612 (tp30) REVERT: B 174 LYS cc_start: 0.7753 (tttp) cc_final: 0.7504 (tttp) REVERT: B 224 GLN cc_start: 0.6688 (mp10) cc_final: 0.6322 (mp10) REVERT: B 385 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7826 (mtpp) REVERT: B 387 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7518 (pttm) REVERT: B 474 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7712 (ttpt) REVERT: B 498 TYR cc_start: 0.6695 (t80) cc_final: 0.6443 (t80) REVERT: B 567 GLU cc_start: 0.7111 (tp30) cc_final: 0.6713 (tp30) REVERT: B 569 SER cc_start: 0.8120 (m) cc_final: 0.7893 (m) REVERT: B 582 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7128 (mm-30) REVERT: B 599 ASP cc_start: 0.7658 (t0) cc_final: 0.7270 (t0) REVERT: B 617 ASN cc_start: 0.8041 (m-40) cc_final: 0.7828 (m-40) REVERT: B 624 GLN cc_start: 0.7902 (mm110) cc_final: 0.7684 (mt0) REVERT: B 625 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7715 (mmt-90) REVERT: B 656 ASP cc_start: 0.7387 (m-30) cc_final: 0.6977 (m-30) REVERT: B 722 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7692 (t) REVERT: B 843 ILE cc_start: 0.8815 (mm) cc_final: 0.8425 (mt) REVERT: B 844 TRP cc_start: 0.8316 (m-90) cc_final: 0.7917 (m-10) REVERT: B 848 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6869 (mm-30) REVERT: B 898 LYS cc_start: 0.7904 (mmmm) cc_final: 0.7620 (mmmm) REVERT: B 904 ASP cc_start: 0.7632 (t0) cc_final: 0.7306 (t0) REVERT: B 911 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7624 (mtt180) REVERT: C 120 PHE cc_start: 0.7810 (m-80) cc_final: 0.7518 (m-80) REVERT: C 171 GLU cc_start: 0.6876 (tp30) cc_final: 0.6535 (tp30) REVERT: C 174 LYS cc_start: 0.7673 (tttp) cc_final: 0.7441 (tttp) REVERT: C 314 TYR cc_start: 0.7928 (m-80) cc_final: 0.7589 (m-80) REVERT: C 356 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7263 (mttp) REVERT: C 380 THR cc_start: 0.8164 (t) cc_final: 0.7761 (p) REVERT: C 474 LYS cc_start: 0.8000 (ttpt) cc_final: 0.7712 (ttpt) REVERT: C 539 ASP cc_start: 0.6959 (p0) cc_final: 0.6734 (p0) REVERT: C 569 SER cc_start: 0.8204 (m) cc_final: 0.7703 (p) REVERT: C 624 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7685 (mt0) REVERT: C 627 TYR cc_start: 0.7808 (m-80) cc_final: 0.7565 (m-80) REVERT: C 643 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8124 (mtpp) REVERT: C 656 ASP cc_start: 0.7135 (m-30) cc_final: 0.6719 (m-30) REVERT: C 759 SER cc_start: 0.7975 (m) cc_final: 0.7714 (p) REVERT: C 844 TRP cc_start: 0.8124 (m-90) cc_final: 0.7903 (m-10) REVERT: C 898 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7498 (mmmm) REVERT: C 901 SER cc_start: 0.8457 (t) cc_final: 0.7925 (p) REVERT: C 904 ASP cc_start: 0.7571 (t0) cc_final: 0.7278 (t0) REVERT: D 171 GLU cc_start: 0.6908 (tp30) cc_final: 0.6608 (tp30) REVERT: D 174 LYS cc_start: 0.7733 (tttp) cc_final: 0.7469 (tttp) REVERT: D 241 LYS cc_start: 0.7414 (mmmm) cc_final: 0.7146 (mmmm) REVERT: D 303 PHE cc_start: 0.7371 (t80) cc_final: 0.7073 (t80) REVERT: D 474 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7577 (ttpt) REVERT: D 481 LEU cc_start: 0.7304 (mm) cc_final: 0.7020 (mp) REVERT: D 498 TYR cc_start: 0.6799 (t80) cc_final: 0.6516 (t80) REVERT: D 539 ASP cc_start: 0.7111 (p0) cc_final: 0.6847 (p0) REVERT: D 548 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7493 (mtpp) REVERT: D 558 THR cc_start: 0.8100 (m) cc_final: 0.7659 (t) REVERT: D 567 GLU cc_start: 0.7057 (tp30) cc_final: 0.6715 (tp30) REVERT: D 569 SER cc_start: 0.8196 (m) cc_final: 0.7692 (p) REVERT: D 582 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7195 (mm-30) REVERT: D 595 SER cc_start: 0.8696 (p) cc_final: 0.8299 (p) REVERT: D 599 ASP cc_start: 0.7698 (m-30) cc_final: 0.7476 (m-30) REVERT: D 615 LYS cc_start: 0.8483 (mtpp) cc_final: 0.7854 (mtmt) REVERT: D 656 ASP cc_start: 0.7211 (m-30) cc_final: 0.6787 (m-30) REVERT: D 679 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7922 (mtpp) REVERT: D 730 ASP cc_start: 0.7022 (t0) cc_final: 0.6784 (t0) REVERT: D 833 LEU cc_start: 0.8330 (tt) cc_final: 0.8090 (tp) REVERT: D 898 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7679 (mmmm) REVERT: D 901 SER cc_start: 0.8447 (t) cc_final: 0.7916 (p) REVERT: D 904 ASP cc_start: 0.7610 (t0) cc_final: 0.7262 (t0) REVERT: D 917 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7135 (tm-30) REVERT: E 171 GLU cc_start: 0.7050 (tp30) cc_final: 0.6780 (tp30) REVERT: E 252 LYS cc_start: 0.7268 (tptt) cc_final: 0.6920 (tptt) REVERT: E 355 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7844 (ttmt) REVERT: E 357 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7715 (mmmm) REVERT: E 498 TYR cc_start: 0.6824 (t80) cc_final: 0.6586 (t80) REVERT: E 558 THR cc_start: 0.8083 (m) cc_final: 0.7724 (t) REVERT: E 569 SER cc_start: 0.8199 (m) cc_final: 0.7992 (m) REVERT: E 582 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7031 (mm-30) REVERT: E 599 ASP cc_start: 0.7774 (t0) cc_final: 0.7457 (m-30) REVERT: E 605 ASP cc_start: 0.6857 (m-30) cc_final: 0.6609 (t0) REVERT: E 631 MET cc_start: 0.7339 (tpp) cc_final: 0.7014 (mtp) REVERT: E 656 ASP cc_start: 0.7305 (m-30) cc_final: 0.6890 (m-30) REVERT: E 667 LEU cc_start: 0.8173 (mt) cc_final: 0.7847 (mt) REVERT: E 843 ILE cc_start: 0.8754 (mm) cc_final: 0.8496 (mt) REVERT: E 878 LEU cc_start: 0.8069 (mp) cc_final: 0.7808 (mp) REVERT: E 898 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7516 (mmmm) REVERT: E 901 SER cc_start: 0.8410 (t) cc_final: 0.7880 (p) REVERT: E 904 ASP cc_start: 0.7441 (t0) cc_final: 0.7139 (t0) REVERT: E 917 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7181 (tm-30) REVERT: F 120 PHE cc_start: 0.7917 (m-80) cc_final: 0.7636 (m-10) REVERT: F 171 GLU cc_start: 0.6746 (tp30) cc_final: 0.6431 (tp30) REVERT: F 252 LYS cc_start: 0.7376 (tptt) cc_final: 0.6857 (tptt) REVERT: F 385 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7912 (mtpp) REVERT: F 387 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7499 (pttm) REVERT: F 474 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7478 (ttpt) REVERT: F 501 LYS cc_start: 0.7421 (tptt) cc_final: 0.7024 (tppt) REVERT: F 504 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7297 (tm-30) REVERT: F 505 PHE cc_start: 0.7850 (m-10) cc_final: 0.7501 (m-10) REVERT: F 567 GLU cc_start: 0.7126 (tp30) cc_final: 0.6769 (tp30) REVERT: F 569 SER cc_start: 0.8226 (m) cc_final: 0.7723 (p) REVERT: F 759 SER cc_start: 0.8079 (m) cc_final: 0.7739 (p) REVERT: F 833 LEU cc_start: 0.8204 (tt) cc_final: 0.8003 (tt) REVERT: F 844 TRP cc_start: 0.8399 (m-90) cc_final: 0.7957 (m-10) REVERT: F 848 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6922 (mm-30) REVERT: F 865 PHE cc_start: 0.8232 (t80) cc_final: 0.7882 (t80) REVERT: F 898 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7598 (mmmm) REVERT: F 901 SER cc_start: 0.8486 (t) cc_final: 0.7974 (p) REVERT: F 904 ASP cc_start: 0.7396 (t0) cc_final: 0.7109 (t0) REVERT: F 910 GLN cc_start: 0.7875 (mt0) cc_final: 0.7594 (mt0) outliers start: 115 outliers final: 73 residues processed: 922 average time/residue: 0.4994 time to fit residues: 746.9259 Evaluate side-chains 946 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 866 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain E residue 173 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 714 ASN Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 850 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 1.9990 chunk 428 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 279 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 476 optimal weight: 4.9990 chunk 395 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 157 optimal weight: 0.9980 chunk 249 optimal weight: 0.0870 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 740 ASN A 910 GLN B 95 GLN B 637 ASN B 789 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 806 ASN D 154 ASN E 571 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39198 Z= 0.206 Angle : 0.562 7.686 53256 Z= 0.276 Chirality : 0.041 0.164 6234 Planarity : 0.004 0.061 6708 Dihedral : 7.161 120.324 5328 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.97 % Allowed : 17.13 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4938 helix: 1.53 (0.10), residues: 2544 sheet: -1.23 (0.29), residues: 324 loop : -2.13 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 846 HIS 0.007 0.001 HIS E 701 PHE 0.015 0.001 PHE E 868 TYR 0.039 0.002 TYR D 541 ARG 0.009 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 895 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8076 (m-80) cc_final: 0.7720 (m-80) REVERT: A 171 GLU cc_start: 0.6783 (tp30) cc_final: 0.6421 (tp30) REVERT: A 174 LYS cc_start: 0.7757 (tttp) cc_final: 0.7514 (tttp) REVERT: A 224 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6853 (mp10) REVERT: A 357 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7709 (mmmm) REVERT: A 385 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7673 (mtpp) REVERT: A 387 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7506 (pttm) REVERT: A 474 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7692 (ttpt) REVERT: A 541 TYR cc_start: 0.7388 (t80) cc_final: 0.7180 (t80) REVERT: A 558 THR cc_start: 0.8151 (m) cc_final: 0.7909 (t) REVERT: A 567 GLU cc_start: 0.7102 (tp30) cc_final: 0.6786 (tp30) REVERT: A 569 SER cc_start: 0.8154 (m) cc_final: 0.7666 (p) REVERT: A 599 ASP cc_start: 0.7685 (m-30) cc_final: 0.7459 (m-30) REVERT: A 617 ASN cc_start: 0.8226 (m-40) cc_final: 0.7976 (m-40) REVERT: A 696 ILE cc_start: 0.8495 (pt) cc_final: 0.8263 (pt) REVERT: A 722 VAL cc_start: 0.7938 (OUTLIER) cc_final: 0.7702 (t) REVERT: A 746 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7590 (t) REVERT: A 759 SER cc_start: 0.8135 (m) cc_final: 0.7814 (p) REVERT: A 844 TRP cc_start: 0.8260 (m-90) cc_final: 0.7874 (m-10) REVERT: A 848 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 898 LYS cc_start: 0.7994 (mmmm) cc_final: 0.7485 (mmmm) REVERT: A 901 SER cc_start: 0.8435 (t) cc_final: 0.7726 (p) REVERT: A 904 ASP cc_start: 0.7554 (t0) cc_final: 0.7236 (t0) REVERT: A 917 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7195 (tm-30) REVERT: B 116 PHE cc_start: 0.7703 (t80) cc_final: 0.7444 (t80) REVERT: B 120 PHE cc_start: 0.8171 (m-80) cc_final: 0.7768 (m-80) REVERT: B 171 GLU cc_start: 0.6871 (tp30) cc_final: 0.6620 (tp30) REVERT: B 174 LYS cc_start: 0.7740 (tttp) cc_final: 0.7514 (tttp) REVERT: B 474 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7702 (ttpt) REVERT: B 498 TYR cc_start: 0.6714 (t80) cc_final: 0.6503 (t80) REVERT: B 567 GLU cc_start: 0.7105 (tp30) cc_final: 0.6718 (tp30) REVERT: B 569 SER cc_start: 0.8121 (m) cc_final: 0.7907 (m) REVERT: B 582 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7188 (mm-30) REVERT: B 599 ASP cc_start: 0.7653 (t0) cc_final: 0.7295 (t0) REVERT: B 625 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7686 (mmt-90) REVERT: B 656 ASP cc_start: 0.7396 (m-30) cc_final: 0.7012 (m-30) REVERT: B 722 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7636 (t) REVERT: B 843 ILE cc_start: 0.8788 (mm) cc_final: 0.8381 (mt) REVERT: B 844 TRP cc_start: 0.8331 (m-90) cc_final: 0.7922 (m-10) REVERT: B 848 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6905 (mm-30) REVERT: B 898 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7614 (mmmm) REVERT: B 904 ASP cc_start: 0.7639 (t0) cc_final: 0.7300 (t0) REVERT: B 911 ARG cc_start: 0.8002 (mtt90) cc_final: 0.7645 (mtt180) REVERT: C 120 PHE cc_start: 0.7820 (m-80) cc_final: 0.7488 (m-80) REVERT: C 171 GLU cc_start: 0.6809 (tp30) cc_final: 0.6485 (tp30) REVERT: C 174 LYS cc_start: 0.7700 (tttp) cc_final: 0.7454 (tttp) REVERT: C 314 TYR cc_start: 0.7939 (m-80) cc_final: 0.7688 (m-80) REVERT: C 380 THR cc_start: 0.8172 (t) cc_final: 0.7755 (p) REVERT: C 457 LYS cc_start: 0.7532 (ttmm) cc_final: 0.7150 (mttm) REVERT: C 474 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7684 (ttpt) REVERT: C 539 ASP cc_start: 0.6998 (p0) cc_final: 0.6758 (p0) REVERT: C 569 SER cc_start: 0.8220 (m) cc_final: 0.7725 (p) REVERT: C 570 ARG cc_start: 0.7270 (ttm110) cc_final: 0.7053 (ttm110) REVERT: C 624 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7666 (mt0) REVERT: C 627 TYR cc_start: 0.7821 (m-80) cc_final: 0.7568 (m-80) REVERT: C 643 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8150 (mtpp) REVERT: C 656 ASP cc_start: 0.7133 (m-30) cc_final: 0.6755 (m-30) REVERT: C 759 SER cc_start: 0.7980 (m) cc_final: 0.7726 (p) REVERT: C 844 TRP cc_start: 0.8140 (m-90) cc_final: 0.7897 (m-10) REVERT: C 865 PHE cc_start: 0.8046 (t80) cc_final: 0.7798 (t80) REVERT: C 898 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7441 (mmmm) REVERT: C 901 SER cc_start: 0.8459 (t) cc_final: 0.7946 (p) REVERT: C 904 ASP cc_start: 0.7576 (t0) cc_final: 0.7284 (t0) REVERT: D 171 GLU cc_start: 0.6877 (tp30) cc_final: 0.6571 (tp30) REVERT: D 174 LYS cc_start: 0.7757 (tttp) cc_final: 0.7481 (tttp) REVERT: D 303 PHE cc_start: 0.7382 (t80) cc_final: 0.7079 (t80) REVERT: D 474 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7612 (ttpt) REVERT: D 498 TYR cc_start: 0.6826 (t80) cc_final: 0.6587 (t80) REVERT: D 539 ASP cc_start: 0.7084 (p0) cc_final: 0.6827 (p0) REVERT: D 548 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7478 (mtpp) REVERT: D 558 THR cc_start: 0.8218 (m) cc_final: 0.7785 (t) REVERT: D 567 GLU cc_start: 0.7068 (tp30) cc_final: 0.6727 (tp30) REVERT: D 569 SER cc_start: 0.8210 (m) cc_final: 0.7717 (p) REVERT: D 582 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7208 (mm-30) REVERT: D 595 SER cc_start: 0.8686 (p) cc_final: 0.8308 (p) REVERT: D 599 ASP cc_start: 0.7682 (m-30) cc_final: 0.7473 (m-30) REVERT: D 615 LYS cc_start: 0.8511 (mtpp) cc_final: 0.7858 (mtmt) REVERT: D 656 ASP cc_start: 0.7192 (m-30) cc_final: 0.6758 (m-30) REVERT: D 679 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7905 (mtpp) REVERT: D 730 ASP cc_start: 0.7012 (t0) cc_final: 0.6775 (t0) REVERT: D 898 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7662 (mmmm) REVERT: D 901 SER cc_start: 0.8452 (t) cc_final: 0.7927 (p) REVERT: D 904 ASP cc_start: 0.7622 (t0) cc_final: 0.7254 (t0) REVERT: D 917 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7102 (tm-30) REVERT: E 171 GLU cc_start: 0.7052 (tp30) cc_final: 0.6793 (tp30) REVERT: E 252 LYS cc_start: 0.7342 (tptt) cc_final: 0.6975 (tptt) REVERT: E 474 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7215 (ttpt) REVERT: E 558 THR cc_start: 0.8137 (m) cc_final: 0.7777 (t) REVERT: E 569 SER cc_start: 0.8196 (m) cc_final: 0.7958 (m) REVERT: E 582 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7043 (mm-30) REVERT: E 599 ASP cc_start: 0.7756 (t0) cc_final: 0.7403 (m-30) REVERT: E 656 ASP cc_start: 0.7305 (m-30) cc_final: 0.6891 (m-30) REVERT: E 843 ILE cc_start: 0.8729 (mm) cc_final: 0.8499 (mt) REVERT: E 898 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7545 (mmmm) REVERT: E 901 SER cc_start: 0.8395 (t) cc_final: 0.7920 (p) REVERT: E 904 ASP cc_start: 0.7442 (t0) cc_final: 0.7161 (t0) REVERT: E 917 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7153 (tm-30) REVERT: F 120 PHE cc_start: 0.7926 (m-80) cc_final: 0.7664 (m-10) REVERT: F 162 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6428 (mm-30) REVERT: F 171 GLU cc_start: 0.6711 (tp30) cc_final: 0.6456 (tp30) REVERT: F 252 LYS cc_start: 0.7400 (tptt) cc_final: 0.6850 (tptt) REVERT: F 385 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7896 (mtpp) REVERT: F 387 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7486 (pttm) REVERT: F 474 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7472 (ttpt) REVERT: F 567 GLU cc_start: 0.7123 (tp30) cc_final: 0.6774 (tp30) REVERT: F 569 SER cc_start: 0.8229 (m) cc_final: 0.7733 (p) REVERT: F 624 GLN cc_start: 0.7636 (mt0) cc_final: 0.7334 (mt0) REVERT: F 696 ILE cc_start: 0.8293 (pt) cc_final: 0.8009 (pt) REVERT: F 730 ASP cc_start: 0.7184 (t0) cc_final: 0.6891 (t0) REVERT: F 844 TRP cc_start: 0.8421 (m-90) cc_final: 0.7935 (m-10) REVERT: F 848 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6964 (mm-30) REVERT: F 865 PHE cc_start: 0.8250 (t80) cc_final: 0.7860 (t80) REVERT: F 898 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7572 (mmmm) REVERT: F 901 SER cc_start: 0.8449 (t) cc_final: 0.7942 (p) REVERT: F 904 ASP cc_start: 0.7386 (t0) cc_final: 0.7129 (t0) REVERT: F 910 GLN cc_start: 0.7908 (mt0) cc_final: 0.7642 (mt0) outliers start: 122 outliers final: 86 residues processed: 947 average time/residue: 0.4955 time to fit residues: 758.7931 Evaluate side-chains 966 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 873 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 654 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 271 optimal weight: 0.0770 chunk 347 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 400 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 474 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 637 ASN A 740 ASN A 910 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN C 95 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 683 GLN C 806 ASN D 95 GLN E 95 GLN F 95 GLN F 815 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39198 Z= 0.210 Angle : 0.565 7.402 53256 Z= 0.277 Chirality : 0.042 0.169 6234 Planarity : 0.004 0.058 6708 Dihedral : 7.009 118.197 5328 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.05 % Allowed : 17.88 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4938 helix: 1.55 (0.10), residues: 2556 sheet: -1.47 (0.27), residues: 342 loop : -2.18 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 PHE 0.015 0.001 PHE B 868 TYR 0.033 0.002 TYR D 541 ARG 0.005 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 900 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8085 (m-80) cc_final: 0.7701 (m-80) REVERT: A 171 GLU cc_start: 0.6774 (tp30) cc_final: 0.6421 (tp30) REVERT: A 174 LYS cc_start: 0.7795 (tttp) cc_final: 0.7549 (tttp) REVERT: A 224 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: A 385 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7629 (mtpp) REVERT: A 387 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7491 (pttm) REVERT: A 474 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7658 (ttpt) REVERT: A 558 THR cc_start: 0.8217 (m) cc_final: 0.7998 (t) REVERT: A 567 GLU cc_start: 0.7092 (tp30) cc_final: 0.6791 (tp30) REVERT: A 569 SER cc_start: 0.8152 (m) cc_final: 0.7657 (p) REVERT: A 595 SER cc_start: 0.8684 (p) cc_final: 0.8455 (p) REVERT: A 599 ASP cc_start: 0.7700 (m-30) cc_final: 0.7457 (m-30) REVERT: A 617 ASN cc_start: 0.8187 (m-40) cc_final: 0.7959 (m-40) REVERT: A 695 ARG cc_start: 0.7661 (tpp-160) cc_final: 0.7442 (tpt90) REVERT: A 720 GLU cc_start: 0.7240 (mp0) cc_final: 0.6904 (mp0) REVERT: A 722 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7726 (t) REVERT: A 746 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7563 (t) REVERT: A 759 SER cc_start: 0.8128 (m) cc_final: 0.7792 (p) REVERT: A 844 TRP cc_start: 0.8264 (m-90) cc_final: 0.7995 (m-10) REVERT: A 848 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6746 (mm-30) REVERT: A 898 LYS cc_start: 0.7981 (mmmm) cc_final: 0.7481 (mmmm) REVERT: A 901 SER cc_start: 0.8400 (t) cc_final: 0.7702 (p) REVERT: A 904 ASP cc_start: 0.7542 (t0) cc_final: 0.7271 (t0) REVERT: A 917 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7209 (tm-30) REVERT: B 116 PHE cc_start: 0.7672 (t80) cc_final: 0.7410 (t80) REVERT: B 120 PHE cc_start: 0.8161 (m-80) cc_final: 0.7738 (m-80) REVERT: B 171 GLU cc_start: 0.6863 (tp30) cc_final: 0.6628 (tp30) REVERT: B 174 LYS cc_start: 0.7756 (tttp) cc_final: 0.7537 (tttp) REVERT: B 224 GLN cc_start: 0.6730 (mp10) cc_final: 0.6416 (mp10) REVERT: B 474 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7642 (ttpt) REVERT: B 567 GLU cc_start: 0.7099 (tp30) cc_final: 0.6712 (tp30) REVERT: B 569 SER cc_start: 0.8140 (m) cc_final: 0.7922 (m) REVERT: B 582 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7178 (mm-30) REVERT: B 599 ASP cc_start: 0.7645 (t0) cc_final: 0.7233 (t0) REVERT: B 617 ASN cc_start: 0.8042 (m-40) cc_final: 0.7831 (m-40) REVERT: B 625 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7775 (mmt-90) REVERT: B 656 ASP cc_start: 0.7420 (m-30) cc_final: 0.7014 (m-30) REVERT: B 722 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7613 (t) REVERT: B 843 ILE cc_start: 0.8739 (mm) cc_final: 0.8369 (mt) REVERT: B 844 TRP cc_start: 0.8337 (m-90) cc_final: 0.7933 (m-10) REVERT: B 848 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 898 LYS cc_start: 0.7898 (mmmm) cc_final: 0.7648 (mmmm) REVERT: B 904 ASP cc_start: 0.7588 (t0) cc_final: 0.7265 (t0) REVERT: B 911 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7681 (mtt180) REVERT: C 120 PHE cc_start: 0.7806 (m-80) cc_final: 0.7496 (m-80) REVERT: C 171 GLU cc_start: 0.6789 (tp30) cc_final: 0.6496 (tp30) REVERT: C 174 LYS cc_start: 0.7669 (tttp) cc_final: 0.7442 (tttp) REVERT: C 314 TYR cc_start: 0.7957 (m-80) cc_final: 0.7701 (m-80) REVERT: C 380 THR cc_start: 0.8186 (t) cc_final: 0.7752 (p) REVERT: C 387 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7769 (pttm) REVERT: C 423 ASP cc_start: 0.7830 (t70) cc_final: 0.7442 (t70) REVERT: C 457 LYS cc_start: 0.7617 (ttmm) cc_final: 0.7278 (mttm) REVERT: C 474 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7670 (ttpt) REVERT: C 539 ASP cc_start: 0.6971 (p0) cc_final: 0.6735 (p0) REVERT: C 569 SER cc_start: 0.8210 (m) cc_final: 0.7713 (p) REVERT: C 627 TYR cc_start: 0.7808 (m-80) cc_final: 0.7599 (m-80) REVERT: C 631 MET cc_start: 0.7410 (tpp) cc_final: 0.7162 (mtt) REVERT: C 643 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8164 (mtpp) REVERT: C 759 SER cc_start: 0.7982 (m) cc_final: 0.7726 (p) REVERT: C 844 TRP cc_start: 0.8156 (m-90) cc_final: 0.7890 (m-10) REVERT: C 865 PHE cc_start: 0.8079 (t80) cc_final: 0.7805 (t80) REVERT: C 898 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7566 (mmmm) REVERT: C 904 ASP cc_start: 0.7637 (t0) cc_final: 0.7329 (t0) REVERT: D 171 GLU cc_start: 0.6865 (tp30) cc_final: 0.6572 (tp30) REVERT: D 174 LYS cc_start: 0.7779 (tttp) cc_final: 0.7497 (tttp) REVERT: D 303 PHE cc_start: 0.7373 (t80) cc_final: 0.7066 (t80) REVERT: D 474 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7701 (ttpt) REVERT: D 481 LEU cc_start: 0.7312 (mm) cc_final: 0.7047 (mp) REVERT: D 498 TYR cc_start: 0.6869 (t80) cc_final: 0.6650 (t80) REVERT: D 539 ASP cc_start: 0.7114 (p0) cc_final: 0.6838 (p0) REVERT: D 548 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7420 (mtpp) REVERT: D 558 THR cc_start: 0.8273 (m) cc_final: 0.7855 (t) REVERT: D 567 GLU cc_start: 0.7053 (tp30) cc_final: 0.6760 (tp30) REVERT: D 569 SER cc_start: 0.8200 (m) cc_final: 0.7735 (p) REVERT: D 582 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7213 (mm-30) REVERT: D 595 SER cc_start: 0.8710 (p) cc_final: 0.8323 (p) REVERT: D 599 ASP cc_start: 0.7698 (m-30) cc_final: 0.7480 (m-30) REVERT: D 615 LYS cc_start: 0.8508 (mtpp) cc_final: 0.7768 (mtmt) REVERT: D 656 ASP cc_start: 0.7225 (m-30) cc_final: 0.6800 (m-30) REVERT: D 679 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7926 (mtpp) REVERT: D 730 ASP cc_start: 0.7034 (t0) cc_final: 0.6826 (t0) REVERT: D 746 THR cc_start: 0.7777 (p) cc_final: 0.7419 (t) REVERT: D 834 VAL cc_start: 0.8404 (t) cc_final: 0.8199 (m) REVERT: D 898 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7653 (mmmm) REVERT: D 901 SER cc_start: 0.8414 (t) cc_final: 0.7896 (p) REVERT: D 904 ASP cc_start: 0.7599 (t0) cc_final: 0.7292 (t0) REVERT: D 917 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7071 (tm-30) REVERT: E 168 ILE cc_start: 0.8200 (tp) cc_final: 0.7883 (tp) REVERT: E 171 GLU cc_start: 0.7059 (tp30) cc_final: 0.6840 (tp30) REVERT: E 252 LYS cc_start: 0.7502 (tptt) cc_final: 0.7083 (tptt) REVERT: E 299 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8361 (mt) REVERT: E 357 LYS cc_start: 0.7968 (mmmm) cc_final: 0.7685 (mmmm) REVERT: E 474 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7212 (ttpt) REVERT: E 558 THR cc_start: 0.8211 (m) cc_final: 0.7816 (t) REVERT: E 582 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7120 (mm-30) REVERT: E 599 ASP cc_start: 0.7799 (t0) cc_final: 0.7469 (m-30) REVERT: E 605 ASP cc_start: 0.6942 (m-30) cc_final: 0.6679 (t0) REVERT: E 631 MET cc_start: 0.7320 (tpp) cc_final: 0.7005 (mtt) REVERT: E 656 ASP cc_start: 0.7320 (m-30) cc_final: 0.6901 (m-30) REVERT: E 667 LEU cc_start: 0.8315 (mt) cc_final: 0.7908 (mt) REVERT: E 878 LEU cc_start: 0.7930 (mp) cc_final: 0.7657 (mp) REVERT: E 898 LYS cc_start: 0.7921 (mmmm) cc_final: 0.7543 (mmmm) REVERT: E 901 SER cc_start: 0.8382 (t) cc_final: 0.7881 (p) REVERT: E 904 ASP cc_start: 0.7437 (t0) cc_final: 0.7194 (t0) REVERT: E 907 VAL cc_start: 0.7995 (t) cc_final: 0.7638 (p) REVERT: E 917 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7165 (tm-30) REVERT: F 120 PHE cc_start: 0.7925 (m-80) cc_final: 0.7658 (m-10) REVERT: F 162 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6451 (mm-30) REVERT: F 171 GLU cc_start: 0.6693 (tp30) cc_final: 0.6464 (tp30) REVERT: F 252 LYS cc_start: 0.7419 (tptt) cc_final: 0.6864 (tptt) REVERT: F 385 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7872 (mtpp) REVERT: F 387 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7532 (pttm) REVERT: F 474 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7467 (ttpt) REVERT: F 501 LYS cc_start: 0.7379 (tppt) cc_final: 0.7064 (tppt) REVERT: F 567 GLU cc_start: 0.7119 (tp30) cc_final: 0.6782 (tp30) REVERT: F 569 SER cc_start: 0.8236 (m) cc_final: 0.7741 (p) REVERT: F 624 GLN cc_start: 0.7669 (mt0) cc_final: 0.7464 (mt0) REVERT: F 759 SER cc_start: 0.8104 (m) cc_final: 0.7754 (p) REVERT: F 775 THR cc_start: 0.8220 (m) cc_final: 0.7991 (p) REVERT: F 844 TRP cc_start: 0.8429 (m-90) cc_final: 0.7952 (m-10) REVERT: F 865 PHE cc_start: 0.8258 (t80) cc_final: 0.7838 (t80) REVERT: F 898 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7683 (mmmm) REVERT: F 904 ASP cc_start: 0.7384 (t0) cc_final: 0.7146 (t0) REVERT: F 910 GLN cc_start: 0.7901 (mt0) cc_final: 0.7639 (mt0) outliers start: 125 outliers final: 83 residues processed: 950 average time/residue: 0.5057 time to fit residues: 783.0694 Evaluate side-chains 971 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 879 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 850 SER Chi-restraints excluded: chain F residue 896 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 283 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 301 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 372 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 740 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 806 ASN D 815 ASN ** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 815 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39198 Z= 0.194 Angle : 0.567 9.807 53256 Z= 0.277 Chirality : 0.042 0.175 6234 Planarity : 0.004 0.059 6708 Dihedral : 6.887 116.745 5328 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.68 % Allowed : 19.03 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4938 helix: 1.59 (0.10), residues: 2586 sheet: -1.38 (0.27), residues: 342 loop : -2.19 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 PHE 0.014 0.001 PHE E 868 TYR 0.028 0.002 TYR D 541 ARG 0.006 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 889 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8082 (m-80) cc_final: 0.7709 (m-80) REVERT: A 171 GLU cc_start: 0.6775 (tp30) cc_final: 0.6419 (tp30) REVERT: A 224 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6725 (mp10) REVERT: A 385 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7606 (mtpp) REVERT: A 387 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7435 (pttm) REVERT: A 474 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7623 (ttpt) REVERT: A 558 THR cc_start: 0.8270 (m) cc_final: 0.8037 (t) REVERT: A 567 GLU cc_start: 0.7080 (tp30) cc_final: 0.6778 (tp30) REVERT: A 569 SER cc_start: 0.8156 (m) cc_final: 0.7666 (p) REVERT: A 595 SER cc_start: 0.8706 (p) cc_final: 0.8475 (p) REVERT: A 599 ASP cc_start: 0.7682 (m-30) cc_final: 0.7449 (m-30) REVERT: A 605 ASP cc_start: 0.6746 (m-30) cc_final: 0.6456 (t0) REVERT: A 617 ASN cc_start: 0.8174 (m-40) cc_final: 0.7933 (m-40) REVERT: A 695 ARG cc_start: 0.7695 (tpp-160) cc_final: 0.7466 (tpt90) REVERT: A 720 GLU cc_start: 0.7213 (mp0) cc_final: 0.6924 (mp0) REVERT: A 722 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7644 (t) REVERT: A 746 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7560 (t) REVERT: A 759 SER cc_start: 0.8123 (m) cc_final: 0.7783 (p) REVERT: A 844 TRP cc_start: 0.8235 (m-90) cc_final: 0.7939 (m-10) REVERT: A 898 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7466 (mmmm) REVERT: A 901 SER cc_start: 0.8395 (t) cc_final: 0.7697 (p) REVERT: A 904 ASP cc_start: 0.7531 (t0) cc_final: 0.7307 (t0) REVERT: A 917 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 116 PHE cc_start: 0.7651 (t80) cc_final: 0.7379 (t80) REVERT: B 120 PHE cc_start: 0.8161 (m-80) cc_final: 0.7739 (m-80) REVERT: B 171 GLU cc_start: 0.6841 (tp30) cc_final: 0.6612 (tp30) REVERT: B 174 LYS cc_start: 0.7788 (tttp) cc_final: 0.7568 (tttp) REVERT: B 474 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7633 (ttpt) REVERT: B 539 ASP cc_start: 0.7018 (p0) cc_final: 0.6787 (p0) REVERT: B 567 GLU cc_start: 0.7091 (tp30) cc_final: 0.6743 (tp30) REVERT: B 569 SER cc_start: 0.8150 (m) cc_final: 0.7916 (m) REVERT: B 582 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 599 ASP cc_start: 0.7618 (t0) cc_final: 0.7207 (t0) REVERT: B 617 ASN cc_start: 0.7999 (m-40) cc_final: 0.7778 (m-40) REVERT: B 625 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7805 (mmt-90) REVERT: B 631 MET cc_start: 0.7326 (tpp) cc_final: 0.6975 (mtp) REVERT: B 656 ASP cc_start: 0.7423 (m-30) cc_final: 0.6998 (m-30) REVERT: B 722 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7634 (t) REVERT: B 843 ILE cc_start: 0.8728 (mm) cc_final: 0.8384 (mt) REVERT: B 844 TRP cc_start: 0.8314 (m-90) cc_final: 0.7961 (m-10) REVERT: B 848 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6974 (mm-30) REVERT: B 898 LYS cc_start: 0.7937 (mmmm) cc_final: 0.7581 (mmmm) REVERT: B 904 ASP cc_start: 0.7578 (t0) cc_final: 0.7278 (t0) REVERT: B 911 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7681 (mtt180) REVERT: C 120 PHE cc_start: 0.7809 (m-80) cc_final: 0.7490 (m-80) REVERT: C 171 GLU cc_start: 0.6773 (tp30) cc_final: 0.6483 (tp30) REVERT: C 174 LYS cc_start: 0.7677 (tttp) cc_final: 0.7429 (tttp) REVERT: C 314 TYR cc_start: 0.7957 (m-80) cc_final: 0.7700 (m-80) REVERT: C 380 THR cc_start: 0.8203 (t) cc_final: 0.7805 (p) REVERT: C 387 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7733 (pttm) REVERT: C 405 MET cc_start: 0.6955 (ptp) cc_final: 0.6732 (ptt) REVERT: C 423 ASP cc_start: 0.7825 (t70) cc_final: 0.7426 (t70) REVERT: C 457 LYS cc_start: 0.7638 (ttmm) cc_final: 0.7294 (mttm) REVERT: C 474 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7596 (ttpt) REVERT: C 539 ASP cc_start: 0.6964 (p0) cc_final: 0.6733 (p0) REVERT: C 569 SER cc_start: 0.8185 (m) cc_final: 0.7706 (p) REVERT: C 643 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8173 (mtpp) REVERT: C 759 SER cc_start: 0.7978 (m) cc_final: 0.7743 (p) REVERT: C 844 TRP cc_start: 0.8146 (m-90) cc_final: 0.7879 (m-10) REVERT: C 865 PHE cc_start: 0.8070 (t80) cc_final: 0.7797 (t80) REVERT: C 904 ASP cc_start: 0.7592 (t0) cc_final: 0.7302 (t0) REVERT: D 171 GLU cc_start: 0.6854 (tp30) cc_final: 0.6567 (tp30) REVERT: D 174 LYS cc_start: 0.7785 (tttp) cc_final: 0.7490 (tttp) REVERT: D 303 PHE cc_start: 0.7375 (t80) cc_final: 0.7073 (t80) REVERT: D 474 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7702 (ttpt) REVERT: D 539 ASP cc_start: 0.7133 (p0) cc_final: 0.6854 (p0) REVERT: D 548 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7434 (mtpp) REVERT: D 558 THR cc_start: 0.8281 (m) cc_final: 0.7881 (t) REVERT: D 567 GLU cc_start: 0.7031 (tp30) cc_final: 0.6750 (tp30) REVERT: D 569 SER cc_start: 0.8209 (m) cc_final: 0.7750 (p) REVERT: D 582 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 595 SER cc_start: 0.8703 (p) cc_final: 0.8326 (p) REVERT: D 599 ASP cc_start: 0.7687 (m-30) cc_final: 0.7483 (m-30) REVERT: D 615 LYS cc_start: 0.8480 (mtpp) cc_final: 0.7794 (mtmt) REVERT: D 624 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7574 (mt0) REVERT: D 656 ASP cc_start: 0.7198 (m-30) cc_final: 0.6777 (m-30) REVERT: D 663 ASP cc_start: 0.6932 (m-30) cc_final: 0.6694 (m-30) REVERT: D 679 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7911 (mtpp) REVERT: D 746 THR cc_start: 0.7765 (p) cc_final: 0.7404 (t) REVERT: D 898 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7641 (mmmm) REVERT: D 901 SER cc_start: 0.8406 (t) cc_final: 0.7888 (p) REVERT: D 904 ASP cc_start: 0.7597 (t0) cc_final: 0.7316 (t0) REVERT: D 917 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6949 (tm-30) REVERT: E 168 ILE cc_start: 0.8168 (tp) cc_final: 0.7852 (tp) REVERT: E 171 GLU cc_start: 0.7047 (tp30) cc_final: 0.6843 (tp30) REVERT: E 252 LYS cc_start: 0.7516 (tptt) cc_final: 0.7047 (tptt) REVERT: E 299 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8356 (mt) REVERT: E 357 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7728 (mmmm) REVERT: E 474 LYS cc_start: 0.7740 (ttpt) cc_final: 0.7161 (ttpt) REVERT: E 558 THR cc_start: 0.8215 (m) cc_final: 0.7863 (t) REVERT: E 582 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7097 (mm-30) REVERT: E 605 ASP cc_start: 0.6853 (m-30) cc_final: 0.6599 (t0) REVERT: E 631 MET cc_start: 0.7358 (tpp) cc_final: 0.7029 (mtp) REVERT: E 638 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6736 (p0) REVERT: E 656 ASP cc_start: 0.7333 (m-30) cc_final: 0.6893 (m-30) REVERT: E 667 LEU cc_start: 0.8318 (mt) cc_final: 0.7925 (mt) REVERT: E 848 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6990 (mm-30) REVERT: E 878 LEU cc_start: 0.7954 (mp) cc_final: 0.7669 (mp) REVERT: E 898 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7554 (mmmm) REVERT: E 901 SER cc_start: 0.8376 (t) cc_final: 0.7856 (p) REVERT: E 904 ASP cc_start: 0.7421 (t0) cc_final: 0.7209 (t0) REVERT: E 907 VAL cc_start: 0.7986 (t) cc_final: 0.7723 (p) REVERT: E 917 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7136 (tm-30) REVERT: F 120 PHE cc_start: 0.7934 (m-80) cc_final: 0.7656 (m-10) REVERT: F 162 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6445 (mm-30) REVERT: F 171 GLU cc_start: 0.6692 (tp30) cc_final: 0.6465 (tp30) REVERT: F 252 LYS cc_start: 0.7423 (tptt) cc_final: 0.6857 (tptt) REVERT: F 385 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7869 (mtpp) REVERT: F 386 ASN cc_start: 0.7426 (t0) cc_final: 0.7216 (t0) REVERT: F 387 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7592 (pttm) REVERT: F 474 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7450 (ttpt) REVERT: F 567 GLU cc_start: 0.7130 (tp30) cc_final: 0.6815 (tp30) REVERT: F 569 SER cc_start: 0.8224 (m) cc_final: 0.7738 (p) REVERT: F 624 GLN cc_start: 0.7682 (mt0) cc_final: 0.7456 (mt0) REVERT: F 638 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6769 (p0) REVERT: F 759 SER cc_start: 0.8090 (m) cc_final: 0.7741 (p) REVERT: F 775 THR cc_start: 0.8183 (m) cc_final: 0.7959 (p) REVERT: F 844 TRP cc_start: 0.8424 (m-90) cc_final: 0.7944 (m-10) REVERT: F 848 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6963 (mm-30) REVERT: F 865 PHE cc_start: 0.8246 (t80) cc_final: 0.7810 (t80) REVERT: F 898 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7669 (mmmm) REVERT: F 904 ASP cc_start: 0.7388 (t0) cc_final: 0.7140 (t0) REVERT: F 910 GLN cc_start: 0.7896 (mt0) cc_final: 0.7644 (mt0) REVERT: F 917 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7035 (tm-30) outliers start: 110 outliers final: 81 residues processed: 936 average time/residue: 0.5076 time to fit residues: 775.1671 Evaluate side-chains 966 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 874 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 899 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain E residue 688 MET Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 896 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 0.9990 chunk 454 optimal weight: 7.9990 chunk 414 optimal weight: 20.0000 chunk 441 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 346 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 399 optimal weight: 1.9990 chunk 417 optimal weight: 0.7980 chunk 440 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN B 899 GLN C 111 ASN C 154 ASN D 317 ASN D 806 ASN D 815 ASN E 571 GLN F 815 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 39198 Z= 0.300 Angle : 0.602 10.337 53256 Z= 0.297 Chirality : 0.043 0.182 6234 Planarity : 0.004 0.058 6708 Dihedral : 6.934 117.002 5328 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.66 % Allowed : 19.13 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4938 helix: 1.40 (0.10), residues: 2592 sheet: -1.44 (0.27), residues: 342 loop : -2.24 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 846 HIS 0.007 0.001 HIS E 701 PHE 0.025 0.001 PHE C 303 TYR 0.056 0.002 TYR B 541 ARG 0.007 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 918 time to evaluate : 4.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8095 (m-80) cc_final: 0.7715 (m-80) REVERT: A 171 GLU cc_start: 0.6785 (tp30) cc_final: 0.6414 (tp30) REVERT: A 202 LEU cc_start: 0.7022 (mt) cc_final: 0.6795 (mp) REVERT: A 385 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7584 (mtpp) REVERT: A 387 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7447 (pttm) REVERT: A 474 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7592 (ttpt) REVERT: A 558 THR cc_start: 0.8327 (m) cc_final: 0.8084 (t) REVERT: A 567 GLU cc_start: 0.7120 (tp30) cc_final: 0.6798 (tp30) REVERT: A 569 SER cc_start: 0.8138 (m) cc_final: 0.7665 (p) REVERT: A 582 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 595 SER cc_start: 0.8732 (p) cc_final: 0.8499 (p) REVERT: A 599 ASP cc_start: 0.7722 (m-30) cc_final: 0.7479 (m-30) REVERT: A 605 ASP cc_start: 0.6843 (m-30) cc_final: 0.6530 (t0) REVERT: A 695 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7493 (tpt90) REVERT: A 720 GLU cc_start: 0.7196 (mp0) cc_final: 0.6938 (mp0) REVERT: A 722 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7703 (t) REVERT: A 746 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7560 (t) REVERT: A 759 SER cc_start: 0.8138 (m) cc_final: 0.7798 (p) REVERT: A 898 LYS cc_start: 0.7999 (mmmm) cc_final: 0.7556 (mmmm) REVERT: A 901 SER cc_start: 0.8387 (t) cc_final: 0.7703 (p) REVERT: A 904 ASP cc_start: 0.7542 (t0) cc_final: 0.7320 (t0) REVERT: A 917 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 116 PHE cc_start: 0.7668 (t80) cc_final: 0.7400 (t80) REVERT: B 120 PHE cc_start: 0.8156 (m-80) cc_final: 0.7772 (m-80) REVERT: B 171 GLU cc_start: 0.6873 (tp30) cc_final: 0.6628 (tp30) REVERT: B 174 LYS cc_start: 0.7805 (tttp) cc_final: 0.7586 (tttp) REVERT: B 224 GLN cc_start: 0.6799 (mp10) cc_final: 0.6527 (mp10) REVERT: B 252 LYS cc_start: 0.7466 (tptt) cc_final: 0.6985 (tptt) REVERT: B 474 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7658 (ttpt) REVERT: B 567 GLU cc_start: 0.7134 (tp30) cc_final: 0.6713 (tp30) REVERT: B 569 SER cc_start: 0.8150 (m) cc_final: 0.7932 (m) REVERT: B 582 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7243 (mm-30) REVERT: B 599 ASP cc_start: 0.7690 (t0) cc_final: 0.7250 (t0) REVERT: B 617 ASN cc_start: 0.8043 (m-40) cc_final: 0.7812 (m-40) REVERT: B 625 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7769 (mmt-90) REVERT: B 656 ASP cc_start: 0.7418 (m-30) cc_final: 0.7010 (m-30) REVERT: B 722 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7677 (t) REVERT: B 843 ILE cc_start: 0.8728 (mm) cc_final: 0.8479 (mt) REVERT: B 848 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7008 (mm-30) REVERT: B 878 LEU cc_start: 0.7932 (mp) cc_final: 0.7701 (mp) REVERT: B 898 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7540 (mmmm) REVERT: B 904 ASP cc_start: 0.7585 (t0) cc_final: 0.7321 (t0) REVERT: B 910 GLN cc_start: 0.7915 (mt0) cc_final: 0.7668 (mt0) REVERT: B 911 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7799 (mtt180) REVERT: B 917 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7113 (tm-30) REVERT: C 120 PHE cc_start: 0.7806 (m-80) cc_final: 0.7482 (m-80) REVERT: C 162 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6518 (mm-30) REVERT: C 171 GLU cc_start: 0.6798 (tp30) cc_final: 0.6509 (tp30) REVERT: C 174 LYS cc_start: 0.7711 (tttp) cc_final: 0.7438 (tttp) REVERT: C 314 TYR cc_start: 0.8015 (m-80) cc_final: 0.7785 (m-80) REVERT: C 380 THR cc_start: 0.8210 (t) cc_final: 0.7784 (p) REVERT: C 387 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7719 (pttm) REVERT: C 403 ASP cc_start: 0.5511 (t70) cc_final: 0.4871 (t0) REVERT: C 405 MET cc_start: 0.6945 (ptp) cc_final: 0.6735 (ptt) REVERT: C 423 ASP cc_start: 0.7830 (t70) cc_final: 0.7427 (t70) REVERT: C 457 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7362 (mttm) REVERT: C 474 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7636 (ttpt) REVERT: C 539 ASP cc_start: 0.6987 (p0) cc_final: 0.6742 (p0) REVERT: C 569 SER cc_start: 0.8182 (m) cc_final: 0.7852 (t) REVERT: C 620 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6858 (tm-30) REVERT: C 624 GLN cc_start: 0.7591 (mt0) cc_final: 0.7352 (mt0) REVERT: C 643 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8161 (mtpp) REVERT: C 730 ASP cc_start: 0.7285 (t0) cc_final: 0.7076 (t0) REVERT: C 759 SER cc_start: 0.7993 (m) cc_final: 0.7758 (p) REVERT: C 826 GLN cc_start: 0.7714 (mp10) cc_final: 0.7409 (mp10) REVERT: C 844 TRP cc_start: 0.8178 (m-90) cc_final: 0.7897 (m-10) REVERT: C 904 ASP cc_start: 0.7612 (t0) cc_final: 0.7339 (t0) REVERT: C 917 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7047 (tm-30) REVERT: D 171 GLU cc_start: 0.6832 (tp30) cc_final: 0.6545 (tp30) REVERT: D 174 LYS cc_start: 0.7801 (tttp) cc_final: 0.7510 (tttp) REVERT: D 303 PHE cc_start: 0.7364 (t80) cc_final: 0.7065 (t80) REVERT: D 474 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7615 (ttpt) REVERT: D 539 ASP cc_start: 0.7184 (p0) cc_final: 0.6948 (p0) REVERT: D 558 THR cc_start: 0.8346 (m) cc_final: 0.7946 (t) REVERT: D 567 GLU cc_start: 0.7083 (tp30) cc_final: 0.6797 (tp30) REVERT: D 569 SER cc_start: 0.8193 (m) cc_final: 0.7748 (p) REVERT: D 582 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7235 (mm-30) REVERT: D 595 SER cc_start: 0.8742 (p) cc_final: 0.8347 (p) REVERT: D 599 ASP cc_start: 0.7731 (m-30) cc_final: 0.7513 (m-30) REVERT: D 615 LYS cc_start: 0.8547 (mtpp) cc_final: 0.7909 (mtmt) REVERT: D 624 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7540 (mt0) REVERT: D 656 ASP cc_start: 0.7230 (m-30) cc_final: 0.6766 (m-30) REVERT: D 663 ASP cc_start: 0.6951 (m-30) cc_final: 0.6721 (m-30) REVERT: D 746 THR cc_start: 0.7752 (p) cc_final: 0.7392 (t) REVERT: D 898 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7641 (mmmm) REVERT: D 901 SER cc_start: 0.8418 (t) cc_final: 0.7895 (p) REVERT: D 904 ASP cc_start: 0.7596 (t0) cc_final: 0.7316 (t0) REVERT: D 917 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6986 (tm-30) REVERT: E 168 ILE cc_start: 0.8261 (tp) cc_final: 0.7949 (tp) REVERT: E 171 GLU cc_start: 0.7066 (tp30) cc_final: 0.6858 (tp30) REVERT: E 252 LYS cc_start: 0.7607 (tptt) cc_final: 0.7094 (tptt) REVERT: E 299 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8373 (mt) REVERT: E 357 LYS cc_start: 0.8010 (mmmm) cc_final: 0.7750 (mmmm) REVERT: E 361 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7826 (tp40) REVERT: E 474 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7132 (ttpt) REVERT: E 481 LEU cc_start: 0.7254 (mm) cc_final: 0.7044 (mp) REVERT: E 539 ASP cc_start: 0.7154 (p0) cc_final: 0.6885 (p0) REVERT: E 558 THR cc_start: 0.8241 (m) cc_final: 0.7894 (t) REVERT: E 582 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7170 (mm-30) REVERT: E 599 ASP cc_start: 0.7791 (t0) cc_final: 0.7469 (m-30) REVERT: E 605 ASP cc_start: 0.6911 (m-30) cc_final: 0.6648 (t0) REVERT: E 638 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6820 (p0) REVERT: E 656 ASP cc_start: 0.7323 (m-30) cc_final: 0.6903 (m-30) REVERT: E 667 LEU cc_start: 0.8414 (mt) cc_final: 0.7983 (mt) REVERT: E 878 LEU cc_start: 0.7970 (mp) cc_final: 0.7703 (mp) REVERT: E 898 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7571 (mmmm) REVERT: E 901 SER cc_start: 0.8377 (t) cc_final: 0.7914 (p) REVERT: E 904 ASP cc_start: 0.7468 (t0) cc_final: 0.7262 (t0) REVERT: E 907 VAL cc_start: 0.8063 (t) cc_final: 0.7799 (p) REVERT: E 917 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7184 (tm-30) REVERT: F 120 PHE cc_start: 0.7936 (m-80) cc_final: 0.7676 (m-80) REVERT: F 162 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6518 (mm-30) REVERT: F 171 GLU cc_start: 0.6682 (tp30) cc_final: 0.6433 (tp30) REVERT: F 252 LYS cc_start: 0.7498 (tptt) cc_final: 0.6907 (tptt) REVERT: F 385 LYS cc_start: 0.8330 (mtpp) cc_final: 0.8005 (mtpp) REVERT: F 387 LYS cc_start: 0.7941 (pttm) cc_final: 0.7630 (pttm) REVERT: F 403 ASP cc_start: 0.5551 (t70) cc_final: 0.4804 (t0) REVERT: F 474 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7423 (ttpt) REVERT: F 567 GLU cc_start: 0.7142 (tp30) cc_final: 0.6815 (tp30) REVERT: F 569 SER cc_start: 0.8238 (m) cc_final: 0.7750 (p) REVERT: F 617 ASN cc_start: 0.8232 (m-40) cc_final: 0.8026 (m-40) REVERT: F 624 GLN cc_start: 0.7698 (mt0) cc_final: 0.7386 (mt0) REVERT: F 638 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6957 (p0) REVERT: F 759 SER cc_start: 0.8094 (m) cc_final: 0.7745 (p) REVERT: F 775 THR cc_start: 0.8200 (m) cc_final: 0.7974 (p) REVERT: F 844 TRP cc_start: 0.8458 (m-90) cc_final: 0.7859 (m-10) REVERT: F 865 PHE cc_start: 0.8288 (t80) cc_final: 0.7765 (t80) REVERT: F 898 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7661 (mmmm) REVERT: F 904 ASP cc_start: 0.7405 (t0) cc_final: 0.7131 (t0) REVERT: F 910 GLN cc_start: 0.7905 (mt0) cc_final: 0.7648 (mt0) REVERT: F 917 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7090 (tm-30) outliers start: 109 outliers final: 84 residues processed: 963 average time/residue: 0.5004 time to fit residues: 783.4328 Evaluate side-chains 992 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 899 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 899 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain E residue 688 MET Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 740 ASN Chi-restraints excluded: chain F residue 896 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 4.9990 chunk 467 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 490 optimal weight: 0.8980 chunk 451 optimal weight: 0.9980 chunk 390 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 301 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 899 GLN C 910 GLN D 815 ASN E 571 GLN E 624 GLN F 291 ASN F 815 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39198 Z= 0.216 Angle : 0.587 9.938 53256 Z= 0.287 Chirality : 0.042 0.197 6234 Planarity : 0.004 0.058 6708 Dihedral : 6.858 116.934 5328 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.41 % Allowed : 19.66 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 4938 helix: 1.47 (0.10), residues: 2592 sheet: -1.40 (0.27), residues: 342 loop : -2.24 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 PHE 0.028 0.001 PHE C 303 TYR 0.044 0.002 TYR A 541 ARG 0.014 0.000 ARG B 900 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 911 time to evaluate : 4.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8088 (m-80) cc_final: 0.7703 (m-80) REVERT: A 171 GLU cc_start: 0.6788 (tp30) cc_final: 0.6437 (tp30) REVERT: A 385 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7577 (mtpp) REVERT: A 387 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7460 (pttm) REVERT: A 474 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7580 (ttpt) REVERT: A 558 THR cc_start: 0.8319 (m) cc_final: 0.8072 (t) REVERT: A 567 GLU cc_start: 0.7094 (tp30) cc_final: 0.6784 (tp30) REVERT: A 569 SER cc_start: 0.8124 (m) cc_final: 0.7654 (p) REVERT: A 582 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 595 SER cc_start: 0.8725 (p) cc_final: 0.8504 (p) REVERT: A 599 ASP cc_start: 0.7697 (m-30) cc_final: 0.7459 (m-30) REVERT: A 605 ASP cc_start: 0.6784 (m-30) cc_final: 0.6511 (t0) REVERT: A 695 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7472 (tpt90) REVERT: A 720 GLU cc_start: 0.7190 (mp0) cc_final: 0.6877 (mp0) REVERT: A 722 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7601 (t) REVERT: A 746 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7547 (t) REVERT: A 759 SER cc_start: 0.8140 (m) cc_final: 0.7800 (p) REVERT: A 844 TRP cc_start: 0.8216 (m-10) cc_final: 0.8006 (m-10) REVERT: A 898 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7486 (mmmm) REVERT: A 901 SER cc_start: 0.8379 (t) cc_final: 0.7698 (p) REVERT: A 904 ASP cc_start: 0.7525 (t0) cc_final: 0.7310 (t0) REVERT: A 917 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 116 PHE cc_start: 0.7642 (t80) cc_final: 0.7357 (t80) REVERT: B 120 PHE cc_start: 0.8168 (m-80) cc_final: 0.7751 (m-80) REVERT: B 171 GLU cc_start: 0.6868 (tp30) cc_final: 0.6627 (tp30) REVERT: B 174 LYS cc_start: 0.7810 (tttp) cc_final: 0.7581 (tttp) REVERT: B 474 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7643 (ttpt) REVERT: B 567 GLU cc_start: 0.7111 (tp30) cc_final: 0.6679 (tp30) REVERT: B 569 SER cc_start: 0.8146 (m) cc_final: 0.7936 (m) REVERT: B 582 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7222 (mm-30) REVERT: B 617 ASN cc_start: 0.7985 (m-40) cc_final: 0.7748 (m-40) REVERT: B 625 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7843 (mmt-90) REVERT: B 638 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7053 (p0) REVERT: B 656 ASP cc_start: 0.7406 (m-30) cc_final: 0.6984 (m-30) REVERT: B 722 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7641 (t) REVERT: B 843 ILE cc_start: 0.8717 (mm) cc_final: 0.8469 (mt) REVERT: B 848 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7026 (mm-30) REVERT: B 878 LEU cc_start: 0.7885 (mp) cc_final: 0.7671 (mp) REVERT: B 903 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6493 (mt-10) REVERT: B 904 ASP cc_start: 0.7564 (t0) cc_final: 0.7287 (t0) REVERT: B 910 GLN cc_start: 0.7918 (mt0) cc_final: 0.7680 (mt0) REVERT: B 917 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7082 (tm-30) REVERT: C 120 PHE cc_start: 0.7798 (m-80) cc_final: 0.7483 (m-80) REVERT: C 162 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6484 (mm-30) REVERT: C 171 GLU cc_start: 0.6775 (tp30) cc_final: 0.6510 (tp30) REVERT: C 174 LYS cc_start: 0.7710 (tttp) cc_final: 0.7443 (tttp) REVERT: C 314 TYR cc_start: 0.8000 (m-80) cc_final: 0.7746 (m-80) REVERT: C 380 THR cc_start: 0.8223 (t) cc_final: 0.7800 (p) REVERT: C 387 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7729 (pttm) REVERT: C 403 ASP cc_start: 0.5511 (t70) cc_final: 0.5201 (t0) REVERT: C 405 MET cc_start: 0.6936 (ptp) cc_final: 0.6717 (ptt) REVERT: C 423 ASP cc_start: 0.7818 (t70) cc_final: 0.7416 (t70) REVERT: C 457 LYS cc_start: 0.7689 (ttmm) cc_final: 0.7344 (mttm) REVERT: C 474 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7624 (ttpt) REVERT: C 539 ASP cc_start: 0.6951 (p0) cc_final: 0.6710 (p0) REVERT: C 569 SER cc_start: 0.8167 (m) cc_final: 0.7837 (t) REVERT: C 570 ARG cc_start: 0.7272 (ttm110) cc_final: 0.7021 (ttm110) REVERT: C 643 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8153 (mtpp) REVERT: C 730 ASP cc_start: 0.7253 (t0) cc_final: 0.7044 (t0) REVERT: C 759 SER cc_start: 0.8012 (m) cc_final: 0.7747 (p) REVERT: C 844 TRP cc_start: 0.8152 (m-90) cc_final: 0.7879 (m-10) REVERT: C 904 ASP cc_start: 0.7606 (t0) cc_final: 0.7316 (t0) REVERT: C 917 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7019 (tm-30) REVERT: D 171 GLU cc_start: 0.6841 (tp30) cc_final: 0.6561 (tp30) REVERT: D 174 LYS cc_start: 0.7806 (tttp) cc_final: 0.7510 (tttp) REVERT: D 303 PHE cc_start: 0.7353 (t80) cc_final: 0.7073 (t80) REVERT: D 474 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7614 (ttpt) REVERT: D 539 ASP cc_start: 0.7189 (p0) cc_final: 0.6950 (p0) REVERT: D 558 THR cc_start: 0.8337 (m) cc_final: 0.7950 (t) REVERT: D 567 GLU cc_start: 0.7059 (tp30) cc_final: 0.6781 (tp30) REVERT: D 569 SER cc_start: 0.8197 (m) cc_final: 0.7756 (p) REVERT: D 582 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 595 SER cc_start: 0.8734 (p) cc_final: 0.8348 (p) REVERT: D 599 ASP cc_start: 0.7712 (m-30) cc_final: 0.7491 (m-30) REVERT: D 615 LYS cc_start: 0.8513 (mtpp) cc_final: 0.7660 (mtmt) REVERT: D 624 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7532 (mt0) REVERT: D 656 ASP cc_start: 0.7211 (m-30) cc_final: 0.6746 (m-30) REVERT: D 663 ASP cc_start: 0.6927 (m-30) cc_final: 0.6697 (m-30) REVERT: D 679 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7980 (mtpp) REVERT: D 746 THR cc_start: 0.7739 (p) cc_final: 0.7377 (t) REVERT: D 898 LYS cc_start: 0.8026 (mmmm) cc_final: 0.7625 (mmmm) REVERT: D 901 SER cc_start: 0.8401 (t) cc_final: 0.7880 (p) REVERT: D 904 ASP cc_start: 0.7579 (t0) cc_final: 0.7309 (t0) REVERT: D 917 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6949 (tm-30) REVERT: E 168 ILE cc_start: 0.8274 (tp) cc_final: 0.7956 (tp) REVERT: E 252 LYS cc_start: 0.7547 (tptt) cc_final: 0.7053 (tptt) REVERT: E 299 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8368 (mt) REVERT: E 356 LYS cc_start: 0.7746 (mttt) cc_final: 0.7522 (mttm) REVERT: E 357 LYS cc_start: 0.8024 (mmmm) cc_final: 0.7764 (mmmm) REVERT: E 361 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7813 (tp40) REVERT: E 474 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7114 (ttpt) REVERT: E 539 ASP cc_start: 0.7145 (p0) cc_final: 0.6875 (p0) REVERT: E 558 THR cc_start: 0.8231 (m) cc_final: 0.7896 (t) REVERT: E 582 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7128 (mm-30) REVERT: E 605 ASP cc_start: 0.6852 (m-30) cc_final: 0.6576 (t0) REVERT: E 638 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6811 (p0) REVERT: E 656 ASP cc_start: 0.7336 (m-30) cc_final: 0.6912 (m-30) REVERT: E 667 LEU cc_start: 0.8378 (mt) cc_final: 0.7958 (mt) REVERT: E 878 LEU cc_start: 0.7908 (mp) cc_final: 0.7635 (mp) REVERT: E 898 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7554 (mmmm) REVERT: E 901 SER cc_start: 0.8386 (t) cc_final: 0.7907 (p) REVERT: E 904 ASP cc_start: 0.7454 (t0) cc_final: 0.7242 (t0) REVERT: E 907 VAL cc_start: 0.7968 (t) cc_final: 0.7699 (p) REVERT: E 917 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7098 (tm-30) REVERT: F 120 PHE cc_start: 0.7931 (m-80) cc_final: 0.7644 (m-10) REVERT: F 162 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6471 (mm-30) REVERT: F 171 GLU cc_start: 0.6660 (tp30) cc_final: 0.6432 (tp30) REVERT: F 252 LYS cc_start: 0.7480 (tptt) cc_final: 0.6883 (tptt) REVERT: F 385 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7929 (mtpp) REVERT: F 387 LYS cc_start: 0.7940 (pttm) cc_final: 0.7585 (pttm) REVERT: F 403 ASP cc_start: 0.5549 (t70) cc_final: 0.4799 (t0) REVERT: F 474 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7421 (ttpt) REVERT: F 567 GLU cc_start: 0.7111 (tp30) cc_final: 0.6797 (tp30) REVERT: F 569 SER cc_start: 0.8222 (m) cc_final: 0.7748 (p) REVERT: F 617 ASN cc_start: 0.8156 (m-40) cc_final: 0.7920 (m-40) REVERT: F 624 GLN cc_start: 0.7663 (mt0) cc_final: 0.7370 (mt0) REVERT: F 638 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6887 (p0) REVERT: F 759 SER cc_start: 0.8091 (m) cc_final: 0.7760 (p) REVERT: F 775 THR cc_start: 0.8176 (m) cc_final: 0.7957 (p) REVERT: F 844 TRP cc_start: 0.8439 (m-90) cc_final: 0.7925 (m-10) REVERT: F 865 PHE cc_start: 0.8257 (t80) cc_final: 0.7744 (t80) REVERT: F 898 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7637 (mmmm) REVERT: F 904 ASP cc_start: 0.7396 (t0) cc_final: 0.7139 (t0) REVERT: F 910 GLN cc_start: 0.7904 (mt0) cc_final: 0.7644 (mt0) REVERT: F 917 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7050 (tm-30) outliers start: 99 outliers final: 80 residues processed: 957 average time/residue: 0.5064 time to fit residues: 785.8769 Evaluate side-chains 984 residues out of total 4104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 894 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain E residue 688 MET Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 896 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 0.6980 chunk 415 optimal weight: 5.9990 chunk 119 optimal weight: 0.0570 chunk 359 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 390 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 401 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 72 optimal weight: 0.7980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 815 ASN ** F 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 815 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.184017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.147015 restraints weight = 55927.550| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.34 r_work: 0.3492 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 39198 Z= 0.162 Angle : 0.568 8.244 53256 Z= 0.277 Chirality : 0.041 0.211 6234 Planarity : 0.004 0.057 6708 Dihedral : 6.672 118.235 5328 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.17 % Allowed : 20.00 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4938 helix: 1.58 (0.10), residues: 2592 sheet: -1.34 (0.28), residues: 342 loop : -2.21 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 PHE 0.028 0.001 PHE C 303 TYR 0.041 0.002 TYR A 541 ARG 0.031 0.000 ARG E 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12932.47 seconds wall clock time: 230 minutes 22.51 seconds (13822.51 seconds total)