Starting phenix.real_space_refine on Tue Apr 16 15:39:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh5_31986/04_2024/7vh5_31986_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh5_31986/04_2024/7vh5_31986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh5_31986/04_2024/7vh5_31986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh5_31986/04_2024/7vh5_31986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh5_31986/04_2024/7vh5_31986_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh5_31986/04_2024/7vh5_31986_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 186 5.16 5 C 26016 2.51 5 N 6172 2.21 5 O 7190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ASP 493": "OD1" <-> "OD2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A ASP 534": "OD1" <-> "OD2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 883": "OD1" <-> "OD2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ASP 493": "OD1" <-> "OD2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B ASP 534": "OD1" <-> "OD2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B ASP 605": "OD1" <-> "OD2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B ASP 656": "OD1" <-> "OD2" Residue "B ARG 659": "NH1" <-> "NH2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 803": "OE1" <-> "OE2" Residue "B ARG 811": "NH1" <-> "NH2" Residue "B PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 883": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 519": "NH1" <-> "NH2" Residue "C ASP 534": "OD1" <-> "OD2" Residue "C ARG 548": "NH1" <-> "NH2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C ASP 605": "OD1" <-> "OD2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C GLU 620": "OE1" <-> "OE2" Residue "C ASP 656": "OD1" <-> "OD2" Residue "C ARG 659": "NH1" <-> "NH2" Residue "C TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 695": "NH1" <-> "NH2" Residue "C GLU 703": "OE1" <-> "OE2" Residue "C TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 754": "NH1" <-> "NH2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 803": "OE1" <-> "OE2" Residue "C ARG 811": "NH1" <-> "NH2" Residue "C PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 847": "OE1" <-> "OE2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 883": "OD1" <-> "OD2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ASP 493": "OD1" <-> "OD2" Residue "D GLU 499": "OE1" <-> "OE2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 519": "NH1" <-> "NH2" Residue "D ASP 534": "OD1" <-> "OD2" Residue "D ARG 548": "NH1" <-> "NH2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "D GLU 582": "OE1" <-> "OE2" Residue "D GLU 596": "OE1" <-> "OE2" Residue "D ASP 605": "OD1" <-> "OD2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D GLU 620": "OE1" <-> "OE2" Residue "D ASP 656": "OD1" <-> "OD2" Residue "D ARG 659": "NH1" <-> "NH2" Residue "D TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 695": "NH1" <-> "NH2" Residue "D GLU 703": "OE1" <-> "OE2" Residue "D TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 754": "NH1" <-> "NH2" Residue "D PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 803": "OE1" <-> "OE2" Residue "D ARG 811": "NH1" <-> "NH2" Residue "D PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 847": "OE1" <-> "OE2" Residue "D PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 883": "OD1" <-> "OD2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E ARG 315": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 324": "NH1" <-> "NH2" Residue "E GLU 392": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ARG 414": "NH1" <-> "NH2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "E ASP 493": "OD1" <-> "OD2" Residue "E GLU 499": "OE1" <-> "OE2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 519": "NH1" <-> "NH2" Residue "E ASP 534": "OD1" <-> "OD2" Residue "E ARG 548": "NH1" <-> "NH2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E GLU 582": "OE1" <-> "OE2" Residue "E GLU 596": "OE1" <-> "OE2" Residue "E ASP 605": "OD1" <-> "OD2" Residue "E GLU 609": "OE1" <-> "OE2" Residue "E GLU 620": "OE1" <-> "OE2" Residue "E ASP 656": "OD1" <-> "OD2" Residue "E ARG 659": "NH1" <-> "NH2" Residue "E TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 695": "NH1" <-> "NH2" Residue "E GLU 703": "OE1" <-> "OE2" Residue "E TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 754": "NH1" <-> "NH2" Residue "E PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 803": "OE1" <-> "OE2" Residue "E ARG 811": "NH1" <-> "NH2" Residue "E PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 847": "OE1" <-> "OE2" Residue "E PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 883": "OD1" <-> "OD2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "F TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 324": "NH1" <-> "NH2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F ARG 414": "NH1" <-> "NH2" Residue "F ARG 469": "NH1" <-> "NH2" Residue "F ASP 493": "OD1" <-> "OD2" Residue "F GLU 499": "OE1" <-> "OE2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 519": "NH1" <-> "NH2" Residue "F ASP 534": "OD1" <-> "OD2" Residue "F ARG 548": "NH1" <-> "NH2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "F GLU 582": "OE1" <-> "OE2" Residue "F GLU 596": "OE1" <-> "OE2" Residue "F ASP 605": "OD1" <-> "OD2" Residue "F GLU 609": "OE1" <-> "OE2" Residue "F GLU 620": "OE1" <-> "OE2" Residue "F ASP 656": "OD1" <-> "OD2" Residue "F ARG 659": "NH1" <-> "NH2" Residue "F TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 695": "NH1" <-> "NH2" Residue "F GLU 703": "OE1" <-> "OE2" Residue "F TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 754": "NH1" <-> "NH2" Residue "F PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 803": "OE1" <-> "OE2" Residue "F ARG 811": "NH1" <-> "NH2" Residue "F PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 847": "OE1" <-> "OE2" Residue "F PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 883": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39615 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "B" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "C" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "D" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "E" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "F" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "A" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 489 Unusual residues: {'POV': 9, 'SPH': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 19.13, per 1000 atoms: 0.48 Number of scatterers: 39615 At special positions: 0 Unit cell: (175.959, 167.727, 182.133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 186 16.00 P 51 15.00 O 7190 8.00 N 6172 7.00 C 26016 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.21 Conformation dependent library (CDL) restraints added in 6.5 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 42 sheets defined 53.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.28 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.519A pdb=" N LYS A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 141 through 173 removed outlier: 3.570A pdb=" N VAL A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 268 through 280 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.548A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.500A pdb=" N ILE A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 355 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.649A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.978A pdb=" N MET A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 421 through 427 Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.591A pdb=" N GLU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) 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 603 Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.517A pdb=" N TYR A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 617 " --> pdb=" O GLN A 613 " (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: 3.635A pdb=" N SER A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 736 removed outlier: 3.695A pdb=" N PHE A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 778 Processing helix chain 'A' and resid 791 through 810 removed outlier: 3.589A pdb=" N LEU A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 Processing helix chain 'A' and resid 852 through 877 Processing helix chain 'A' and resid 880 through 887 Processing helix chain 'A' and resid 897 through 916 removed outlier: 3.647A pdb=" N GLU A 915 " --> pdb=" O SER A 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.519A pdb=" N LYS B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 137 Processing helix chain 'B' and resid 141 through 173 removed outlier: 3.570A pdb=" N VAL B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 268 through 280 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.548A pdb=" N ILE B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 337 through 355 Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.649A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 369 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 410 removed outlier: 3.979A pdb=" N MET B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 421 through 427 Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 491 through 507 Processing helix chain 'B' and resid 540 through 549 Processing helix chain 'B' and resid 562 through 572 removed outlier: 3.591A pdb=" N GLU B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) 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 603 Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.518A pdb=" N TYR B 616 " --> pdb=" O PRO B 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 617 " --> pdb=" O GLN B 613 " (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: 3.636A pdb=" N SER B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 736 removed outlier: 3.695A pdb=" N PHE B 724 " --> pdb=" O ASP B 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 778 Processing helix chain 'B' and resid 791 through 810 removed outlier: 3.590A pdb=" N LEU B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B 808 " --> pdb=" O ASN B 804 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 809 " --> pdb=" O TRP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 842 Processing helix chain 'B' and resid 852 through 877 Processing helix chain 'B' and resid 880 through 887 Processing helix chain 'B' and resid 897 through 916 removed outlier: 3.647A pdb=" N GLU B 915 " --> pdb=" O SER B 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.518A pdb=" N LYS C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 141 through 173 removed outlier: 3.570A pdb=" N VAL C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 285 through 314 removed outlier: 3.548A pdb=" N ILE C 295 " --> pdb=" O ASN C 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 337 through 355 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.649A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 369 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 410 removed outlier: 3.979A pdb=" N MET C 405 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 421 through 427 Processing helix chain 'C' and resid 477 through 481 Processing helix chain 'C' and resid 491 through 507 Processing helix chain 'C' and resid 540 through 549 Processing helix chain 'C' and resid 562 through 572 removed outlier: 3.591A pdb=" N GLU C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) 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 603 Processing helix chain 'C' and resid 612 through 624 removed outlier: 3.517A pdb=" N TYR C 616 " --> pdb=" O PRO C 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 617 " --> pdb=" O GLN C 613 " (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: 3.636A pdb=" N SER C 699 " --> pdb=" O ARG C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 736 removed outlier: 3.695A pdb=" N PHE C 724 " --> pdb=" O ASP C 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 732 " --> pdb=" O PHE C 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 734 " --> pdb=" O ASP C 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 735 " --> pdb=" O VAL C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 778 Processing helix chain 'C' and resid 791 through 810 removed outlier: 3.589A pdb=" N LEU C 806 " --> pdb=" O THR C 802 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE C 807 " --> pdb=" O GLU C 803 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 808 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 809 " --> pdb=" O TRP C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 842 Processing helix chain 'C' and resid 852 through 877 Processing helix chain 'C' and resid 880 through 887 Processing helix chain 'C' and resid 897 through 916 removed outlier: 3.647A pdb=" N GLU C 915 " --> pdb=" O SER C 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.518A pdb=" N LYS D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'D' and resid 141 through 173 removed outlier: 3.570A pdb=" N VAL D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 268 through 280 Processing helix chain 'D' and resid 285 through 314 removed outlier: 3.548A pdb=" N ILE D 295 " --> pdb=" O ASN D 291 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 337 through 355 Processing helix chain 'D' and resid 363 through 370 removed outlier: 3.651A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 369 " --> pdb=" O ILE D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 410 removed outlier: 3.978A pdb=" N MET D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 406 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 421 through 427 Processing helix chain 'D' and resid 477 through 481 Processing helix chain 'D' and resid 491 through 507 Processing helix chain 'D' and resid 540 through 549 Processing helix chain 'D' and resid 562 through 572 removed outlier: 3.591A pdb=" N GLU D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) 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 603 Processing helix chain 'D' and resid 612 through 624 removed outlier: 3.517A pdb=" N TYR D 616 " --> pdb=" O PRO D 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 617 " --> pdb=" O GLN D 613 " (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: 3.635A pdb=" N SER D 699 " --> pdb=" O ARG D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 736 removed outlier: 3.695A pdb=" N PHE D 724 " --> pdb=" O ASP D 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 732 " --> pdb=" O PHE D 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR D 733 " --> pdb=" O ALA D 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 734 " --> pdb=" O ASP D 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 735 " --> pdb=" O VAL D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 778 Processing helix chain 'D' and resid 791 through 810 removed outlier: 3.590A pdb=" N LEU D 806 " --> pdb=" O THR D 802 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE D 807 " --> pdb=" O GLU D 803 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE D 808 " --> pdb=" O ASN D 804 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 809 " --> pdb=" O TRP D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 842 Processing helix chain 'D' and resid 852 through 877 Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 897 through 916 removed outlier: 3.647A pdb=" N GLU D 915 " --> pdb=" O SER D 911 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.519A pdb=" N LYS E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 137 Processing helix chain 'E' and resid 141 through 173 removed outlier: 3.571A pdb=" N VAL E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 268 through 280 Processing helix chain 'E' and resid 285 through 314 removed outlier: 3.549A pdb=" N ILE E 295 " --> pdb=" O ASN E 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 337 through 355 Processing helix chain 'E' and resid 363 through 370 removed outlier: 3.649A pdb=" N SER E 368 " --> pdb=" O ALA E 365 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 369 " --> pdb=" O ILE E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 410 removed outlier: 3.979A pdb=" N MET E 405 " --> pdb=" O PRO E 401 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'E' and resid 477 through 481 Processing helix chain 'E' and resid 491 through 507 Processing helix chain 'E' and resid 540 through 549 Processing helix chain 'E' and resid 562 through 572 removed outlier: 3.591A pdb=" N GLU E 567 " --> pdb=" O GLY E 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 568 " --> pdb=" O ILE E 564 " (cutoff:3.500A) 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 603 Processing helix chain 'E' and resid 612 through 624 removed outlier: 3.517A pdb=" N TYR E 616 " --> pdb=" O PRO E 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E 617 " --> pdb=" O GLN E 613 " (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: 3.635A pdb=" N SER E 699 " --> pdb=" O ARG E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 736 removed outlier: 3.694A pdb=" N PHE E 724 " --> pdb=" O ASP E 720 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA E 732 " --> pdb=" O PHE E 728 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR E 733 " --> pdb=" O ALA E 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 734 " --> pdb=" O ASP E 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA E 735 " --> pdb=" O VAL E 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 778 Processing helix chain 'E' and resid 791 through 810 removed outlier: 3.589A pdb=" N LEU E 806 " --> pdb=" O THR E 802 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE E 807 " --> pdb=" O GLU E 803 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE E 808 " --> pdb=" O ASN E 804 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 809 " --> pdb=" O TRP E 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 842 Processing helix chain 'E' and resid 852 through 877 Processing helix chain 'E' and resid 880 through 887 Processing helix chain 'E' and resid 897 through 916 removed outlier: 3.647A pdb=" N GLU E 915 " --> pdb=" O SER E 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.519A pdb=" N LYS F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 141 through 173 removed outlier: 3.570A pdb=" N VAL F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 268 through 280 Processing helix chain 'F' and resid 285 through 314 removed outlier: 3.548A pdb=" N ILE F 295 " --> pdb=" O ASN F 291 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.500A pdb=" N ILE F 332 " --> pdb=" O GLY F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 355 Processing helix chain 'F' and resid 363 through 370 removed outlier: 3.649A pdb=" N SER F 368 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU F 369 " --> pdb=" O ILE F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 410 removed outlier: 3.979A pdb=" N MET F 405 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU F 406 " --> pdb=" O ASP F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 421 through 427 Processing helix chain 'F' and resid 477 through 481 Processing helix chain 'F' and resid 491 through 507 Processing helix chain 'F' and resid 540 through 549 Processing helix chain 'F' and resid 562 through 572 removed outlier: 3.590A pdb=" N GLU F 567 " --> pdb=" O GLY F 563 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR F 568 " --> pdb=" O ILE F 564 " (cutoff:3.500A) 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 603 Processing helix chain 'F' and resid 612 through 624 removed outlier: 3.517A pdb=" N TYR F 616 " --> pdb=" O PRO F 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG F 617 " --> pdb=" O GLN F 613 " (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: 3.635A pdb=" N SER F 699 " --> pdb=" O ARG F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 736 removed outlier: 3.695A pdb=" N PHE F 724 " --> pdb=" O ASP F 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA F 732 " --> pdb=" O PHE F 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR F 733 " --> pdb=" O ALA F 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 734 " --> pdb=" O ASP F 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 735 " --> pdb=" O VAL F 731 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 778 Processing helix chain 'F' and resid 791 through 810 removed outlier: 3.589A pdb=" N LEU F 806 " --> pdb=" O THR F 802 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE F 807 " --> pdb=" O GLU F 803 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE F 808 " --> pdb=" O ASN F 804 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE F 809 " --> pdb=" O TRP F 805 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 842 Processing helix chain 'F' and resid 852 through 877 Processing helix chain 'F' and resid 880 through 887 Processing helix chain 'F' and resid 897 through 916 removed outlier: 3.647A pdb=" N GLU F 915 " --> pdb=" O SER F 911 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 179 through 184 Processing sheet with id= B, first strand: chain 'A' and resid 200 through 204 removed outlier: 4.172A pdb=" N ASP A 200 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.613A pdb=" N ARG A 253 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP A 226 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL A 251 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 358 through 360 Processing sheet with id= E, first strand: chain 'A' and resid 553 through 557 removed outlier: 4.864A pdb=" N ASP A 378 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 647 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY A 633 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 649 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.515A pdb=" N VAL A 515 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A 529 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 513 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 511 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 516 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 459 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 447 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU A 463 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 445 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 578 through 580 removed outlier: 7.150A pdb=" N GLY A 606 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 179 through 184 Processing sheet with id= I, first strand: chain 'B' and resid 200 through 204 removed outlier: 4.172A pdb=" N ASP B 200 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.612A pdb=" N ARG B 253 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 251 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 358 through 360 Processing sheet with id= L, first strand: chain 'B' and resid 553 through 557 removed outlier: 4.864A pdb=" N ASP B 378 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR B 647 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY B 633 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 649 " --> pdb=" O GLY B 633 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 388 through 390 removed outlier: 6.515A pdb=" N VAL B 515 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 529 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 513 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG B 511 " --> pdb=" O PRO B 531 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 516 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 459 " --> pdb=" O HIS B 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 447 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 463 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 445 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 578 through 580 removed outlier: 7.151A pdb=" N GLY B 606 " --> pdb=" O TYR B 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 179 through 184 Processing sheet with id= P, first strand: chain 'C' and resid 200 through 204 removed outlier: 4.171A pdb=" N ASP C 200 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.612A pdb=" N ARG C 253 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP C 226 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL C 251 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 358 through 360 Processing sheet with id= S, first strand: chain 'C' and resid 553 through 557 removed outlier: 4.864A pdb=" N ASP C 378 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 647 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY C 633 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 649 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 388 through 390 removed outlier: 6.516A pdb=" N VAL C 515 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 529 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 513 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 511 " --> pdb=" O PRO C 531 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 516 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C 459 " --> pdb=" O HIS C 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 447 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU C 463 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL C 445 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 578 through 580 removed outlier: 7.150A pdb=" N GLY C 606 " --> pdb=" O TYR C 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 179 through 184 Processing sheet with id= W, first strand: chain 'D' and resid 200 through 204 removed outlier: 4.172A pdb=" N ASP D 200 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.612A pdb=" N ARG D 253 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP D 226 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL D 251 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 358 through 360 Processing sheet with id= Z, first strand: chain 'D' and resid 553 through 557 removed outlier: 4.864A pdb=" N ASP D 378 " --> pdb=" O THR D 632 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 647 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY D 633 " --> pdb=" O THR D 647 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE D 649 " --> pdb=" O GLY D 633 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 388 through 390 removed outlier: 6.515A pdb=" N VAL D 515 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL D 529 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU D 513 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG D 511 " --> pdb=" O PRO D 531 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 516 " --> pdb=" O VAL D 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 459 " --> pdb=" O HIS D 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 447 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU D 463 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL D 445 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 578 through 580 removed outlier: 7.149A pdb=" N GLY D 606 " --> pdb=" O TYR D 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 179 through 184 Processing sheet with id= AD, first strand: chain 'E' and resid 200 through 204 removed outlier: 4.171A pdb=" N ASP E 200 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.613A pdb=" N ARG E 253 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP E 226 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL E 251 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 358 through 360 Processing sheet with id= AG, first strand: chain 'E' and resid 553 through 557 removed outlier: 4.864A pdb=" N ASP E 378 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR E 647 " --> pdb=" O MET E 631 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLY E 633 " --> pdb=" O THR E 647 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE E 649 " --> pdb=" O GLY E 633 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 388 through 390 removed outlier: 6.515A pdb=" N VAL E 515 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL E 529 " --> pdb=" O LEU E 513 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU E 513 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG E 511 " --> pdb=" O PRO E 531 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 516 " --> pdb=" O VAL E 473 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 459 " --> pdb=" O HIS E 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU E 447 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU E 463 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL E 445 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 578 through 580 removed outlier: 7.150A pdb=" N GLY E 606 " --> pdb=" O TYR E 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 179 through 184 Processing sheet with id= AK, first strand: chain 'F' and resid 200 through 204 removed outlier: 4.171A pdb=" N ASP F 200 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 237 through 239 removed outlier: 3.613A pdb=" N ARG F 253 " --> pdb=" O GLN F 224 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP F 226 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL F 251 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 358 through 360 Processing sheet with id= AN, first strand: chain 'F' and resid 553 through 557 removed outlier: 4.863A pdb=" N ASP F 378 " --> pdb=" O THR F 632 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 647 " --> pdb=" O MET F 631 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY F 633 " --> pdb=" O THR F 647 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE F 649 " --> pdb=" O GLY F 633 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 388 through 390 removed outlier: 6.516A pdb=" N VAL F 515 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL F 529 " --> pdb=" O LEU F 513 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU F 513 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG F 511 " --> pdb=" O PRO F 531 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA F 516 " --> pdb=" O VAL F 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR F 459 " --> pdb=" O HIS F 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU F 447 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU F 463 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL F 445 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 578 through 580 removed outlier: 7.150A pdb=" N GLY F 606 " --> pdb=" O TYR F 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP 2008 hydrogen bonds defined for protein. 5898 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: 17.42 Time building geometry restraints manager: 17.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6231 1.31 - 1.43: 9858 1.43 - 1.56: 23217 1.56 - 1.68: 638 1.68 - 1.81: 369 Bond restraints: 40313 Sorted by residual: bond pdb=" C31 POV D1003 " pdb=" O31 POV D1003 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C31 POV E1007 " pdb=" O31 POV E1007 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C31 POV C1003 " pdb=" O31 POV C1003 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C31 POV B1003 " pdb=" O31 POV B1003 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C31 POV F1003 " pdb=" O31 POV F1003 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.24e+01 ... (remaining 40308 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.20: 390 103.20 - 110.97: 16439 110.97 - 118.74: 16567 118.74 - 126.51: 20258 126.51 - 134.28: 562 Bond angle restraints: 54216 Sorted by residual: angle pdb=" N VAL E 399 " pdb=" CA VAL E 399 " pdb=" C VAL E 399 " ideal model delta sigma weight residual 110.62 116.54 -5.92 1.02e+00 9.61e-01 3.36e+01 angle pdb=" N VAL B 399 " pdb=" CA VAL B 399 " pdb=" C VAL B 399 " ideal model delta sigma weight residual 110.62 116.50 -5.88 1.02e+00 9.61e-01 3.33e+01 angle pdb=" N VAL D 399 " pdb=" CA VAL D 399 " pdb=" C VAL D 399 " ideal model delta sigma weight residual 110.62 116.48 -5.86 1.02e+00 9.61e-01 3.31e+01 angle pdb=" N VAL A 399 " pdb=" CA VAL A 399 " pdb=" C VAL A 399 " ideal model delta sigma weight residual 110.62 116.48 -5.86 1.02e+00 9.61e-01 3.30e+01 angle pdb=" N VAL F 399 " pdb=" CA VAL F 399 " pdb=" C VAL F 399 " ideal model delta sigma weight residual 110.62 116.47 -5.85 1.02e+00 9.61e-01 3.29e+01 ... (remaining 54211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 22631 27.51 - 55.01: 1493 55.01 - 82.52: 281 82.52 - 110.02: 80 110.02 - 137.53: 2 Dihedral angle restraints: 24487 sinusoidal: 10765 harmonic: 13722 Sorted by residual: dihedral pdb=" C3 SPH F1010 " pdb=" C4 SPH F1010 " pdb=" C5 SPH F1010 " pdb=" C6 SPH F1010 " ideal model delta sinusoidal sigma weight residual 169.51 -52.96 -137.53 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C4 SPH F1010 " pdb=" C5 SPH F1010 " pdb=" C6 SPH F1010 " pdb=" C7 SPH F1010 " ideal model delta sinusoidal sigma weight residual 303.19 172.71 130.48 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" C5 SPH F1010 " pdb=" C3 SPH F1010 " pdb=" C4 SPH F1010 " pdb=" O3 SPH F1010 " ideal model delta sinusoidal sigma weight residual -68.94 22.71 -91.65 1 2.00e+01 2.50e-03 2.47e+01 ... (remaining 24484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5164 0.088 - 0.176: 805 0.176 - 0.264: 71 0.264 - 0.353: 11 0.353 - 0.441: 6 Chirality restraints: 6057 Sorted by residual: chirality pdb=" CG LEU B 698 " pdb=" CB LEU B 698 " pdb=" CD1 LEU B 698 " pdb=" CD2 LEU B 698 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CG LEU F 698 " pdb=" CB LEU F 698 " pdb=" CD1 LEU F 698 " pdb=" CD2 LEU F 698 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CG LEU A 698 " pdb=" CB LEU A 698 " pdb=" CD1 LEU A 698 " pdb=" CD2 LEU A 698 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 6054 not shown) Planarity restraints: 6603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 397 " -0.025 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C GLU C 397 " 0.086 2.00e-02 2.50e+03 pdb=" O GLU C 397 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY C 398 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 397 " -0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C GLU A 397 " 0.086 2.00e-02 2.50e+03 pdb=" O GLU A 397 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY A 398 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 397 " -0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C GLU F 397 " 0.086 2.00e-02 2.50e+03 pdb=" O GLU F 397 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY F 398 " -0.029 2.00e-02 2.50e+03 ... (remaining 6600 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 16 1.99 - 2.71: 2971 2.71 - 3.44: 54798 3.44 - 4.17: 96564 4.17 - 4.90: 176607 Nonbonded interactions: 330956 Sorted by model distance: nonbonded pdb=" OE2 GLU A 893 " pdb=" CG2 THR B 897 " model vdw 1.257 3.460 nonbonded pdb=" CG2 THR A 897 " pdb=" OE2 GLU F 893 " model vdw 1.258 3.460 nonbonded pdb=" OE2 GLU C 893 " pdb=" CG2 THR D 897 " model vdw 1.260 3.460 nonbonded pdb=" OE2 GLU E 893 " pdb=" CG2 THR F 897 " model vdw 1.266 3.460 nonbonded pdb=" OE2 GLU B 893 " pdb=" CG2 THR C 897 " model vdw 1.349 3.460 ... (remaining 330951 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' and (resid 110 through 918 or resid 1001 through 1008)) selection = chain 'D' selection = (chain 'E' and (resid 110 through 918 or resid 1001 through 1008)) selection = (chain 'F' and (resid 110 through 918 or resid 1001 through 1008)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.780 Check model and map are aligned: 0.650 Set scattering table: 0.410 Process input model: 102.710 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.240 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.017 0.118 40313 Z= 1.076 Angle : 1.531 12.457 54216 Z= 0.676 Chirality : 0.066 0.441 6057 Planarity : 0.006 0.050 6603 Dihedral : 18.951 137.527 15679 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.31 % Allowed : 1.07 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.10), residues: 4788 helix: -2.29 (0.08), residues: 2688 sheet: -0.02 (0.19), residues: 612 loop : -1.22 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 309 HIS 0.013 0.002 HIS D 701 PHE 0.032 0.003 PHE B 816 TYR 0.023 0.003 TYR E 694 ARG 0.009 0.001 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 447 time to evaluate : 4.083 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 152 MET cc_start: 0.7582 (mmt) cc_final: 0.7366 (mmt) REVERT: A 171 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5584 (tm-30) REVERT: A 405 MET cc_start: 0.1965 (ptt) cc_final: 0.0520 (mtt) REVERT: A 433 TYR cc_start: -0.0535 (OUTLIER) cc_final: -0.1770 (m-80) REVERT: A 548 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7736 (mtm-85) REVERT: B 546 GLU cc_start: 0.7768 (tt0) cc_final: 0.7547 (tt0) REVERT: B 736 ILE cc_start: 0.8110 (tp) cc_final: 0.7867 (tp) REVERT: B 896 SER cc_start: 0.8190 (m) cc_final: 0.7979 (t) REVERT: B 899 SER cc_start: 0.8927 (t) cc_final: 0.8712 (p) REVERT: C 118 MET cc_start: 0.4175 (mtm) cc_final: 0.2655 (tpt) REVERT: C 583 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8251 (ttt180) REVERT: C 823 TRP cc_start: 0.7668 (p-90) cc_final: 0.7287 (p-90) REVERT: C 824 GLN cc_start: 0.8036 (mp10) cc_final: 0.7791 (mp-120) REVERT: C 891 MET cc_start: 0.0438 (mtm) cc_final: 0.0083 (mtp) REVERT: C 904 MET cc_start: 0.7533 (mmp) cc_final: 0.7202 (ttm) REVERT: C 917 GLU cc_start: 0.5809 (pt0) cc_final: 0.4794 (pt0) REVERT: D 143 ASP cc_start: 0.4248 (m-30) cc_final: 0.4007 (m-30) REVERT: D 288 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6567 (tt0) REVERT: D 571 GLN cc_start: 0.8168 (mt0) cc_final: 0.7830 (mt0) REVERT: D 582 GLU cc_start: 0.8084 (tp30) cc_final: 0.7837 (tp30) REVERT: D 775 THR cc_start: 0.8670 (m) cc_final: 0.8274 (p) REVERT: E 288 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6888 (tt0) REVERT: E 656 ASP cc_start: 0.7336 (t0) cc_final: 0.7074 (t0) REVERT: E 889 LYS cc_start: 0.7750 (mttm) cc_final: 0.7244 (pttt) REVERT: E 891 MET cc_start: 0.1600 (mtm) cc_final: 0.1010 (tmm) REVERT: F 152 MET cc_start: 0.5365 (mmt) cc_final: 0.4119 (tmm) REVERT: F 791 MET cc_start: 0.8535 (ttm) cc_final: 0.8259 (ttp) REVERT: F 875 GLU cc_start: 0.6263 (mp0) cc_final: 0.5763 (mp0) REVERT: F 891 MET cc_start: 0.3834 (mtm) cc_final: 0.1812 (mtm) outliers start: 12 outliers final: 1 residues processed: 459 average time/residue: 0.6241 time to fit residues: 460.8795 Evaluate side-chains 321 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 319 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain E residue 435 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 5.9990 chunk 363 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 245 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 376 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 228 optimal weight: 0.9990 chunk 280 optimal weight: 20.0000 chunk 435 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS C 164 GLN D 391 HIS D 542 GLN D 908 GLN F 848 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40313 Z= 0.205 Angle : 0.587 8.656 54216 Z= 0.295 Chirality : 0.041 0.136 6057 Planarity : 0.004 0.037 6603 Dihedral : 17.466 88.750 7309 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.59 % Allowed : 5.57 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.11), residues: 4788 helix: 0.04 (0.09), residues: 2736 sheet: -0.13 (0.21), residues: 480 loop : -1.05 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 756 HIS 0.010 0.001 HIS D 391 PHE 0.019 0.001 PHE B 119 TYR 0.016 0.001 TYR D 352 ARG 0.005 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 361 time to evaluate : 4.080 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 405 MET cc_start: 0.1574 (ptt) cc_final: 0.0214 (mtm) REVERT: A 433 TYR cc_start: -0.0015 (OUTLIER) cc_final: -0.1233 (m-80) REVERT: A 548 ARG cc_start: 0.7767 (ttp-110) cc_final: 0.7541 (mtm-85) REVERT: A 899 SER cc_start: 0.8948 (t) cc_final: 0.8690 (p) REVERT: B 646 ASP cc_start: 0.7609 (m-30) cc_final: 0.7302 (m-30) REVERT: B 736 ILE cc_start: 0.7998 (tp) cc_final: 0.7731 (tp) REVERT: B 761 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8697 (mp) REVERT: B 886 MET cc_start: 0.8076 (mmp) cc_final: 0.7586 (mmt) REVERT: C 823 TRP cc_start: 0.7822 (p-90) cc_final: 0.7407 (p-90) REVERT: C 891 MET cc_start: 0.0244 (mtm) cc_final: -0.0511 (mtm) REVERT: C 903 PHE cc_start: 0.8481 (t80) cc_final: 0.8221 (t80) REVERT: D 571 GLN cc_start: 0.8238 (mt0) cc_final: 0.7858 (mt0) REVERT: D 582 GLU cc_start: 0.8216 (tp30) cc_final: 0.7943 (tp30) REVERT: D 775 THR cc_start: 0.8397 (m) cc_final: 0.8170 (p) REVERT: E 118 MET cc_start: 0.3463 (mtm) cc_final: 0.3262 (mtm) REVERT: E 405 MET cc_start: 0.2965 (ptm) cc_final: 0.1979 (mtp) REVERT: E 889 LYS cc_start: 0.7808 (mttm) cc_final: 0.7118 (pttt) REVERT: E 891 MET cc_start: 0.2097 (mtm) cc_final: 0.1125 (tmm) REVERT: F 118 MET cc_start: 0.4302 (mtt) cc_final: 0.4098 (mtt) REVERT: F 152 MET cc_start: 0.4954 (mmt) cc_final: 0.4287 (tmm) REVERT: F 676 ASP cc_start: 0.7244 (m-30) cc_final: 0.6976 (m-30) REVERT: F 891 MET cc_start: 0.3711 (mtm) cc_final: 0.1856 (mtm) REVERT: F 899 SER cc_start: 0.8851 (t) cc_final: 0.8548 (m) REVERT: F 902 ASP cc_start: 0.7948 (m-30) cc_final: 0.7717 (m-30) REVERT: F 917 GLU cc_start: 0.6015 (tp30) cc_final: 0.4869 (tt0) outliers start: 23 outliers final: 4 residues processed: 372 average time/residue: 0.5311 time to fit residues: 328.0713 Evaluate side-chains 300 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 294 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 538 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 362 optimal weight: 0.0370 chunk 296 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 436 optimal weight: 0.3980 chunk 471 optimal weight: 5.9990 chunk 388 optimal weight: 0.5980 chunk 433 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 350 optimal weight: 3.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 203 GLN B 887 ASN C 203 GLN D 542 GLN D 908 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40313 Z= 0.176 Angle : 0.506 7.304 54216 Z= 0.254 Chirality : 0.040 0.155 6057 Planarity : 0.003 0.034 6603 Dihedral : 15.724 89.939 7305 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.09 % Allowed : 7.56 % Favored : 91.35 % 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: 4788 helix: 1.17 (0.10), residues: 2754 sheet: -0.33 (0.22), residues: 486 loop : -0.82 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 756 HIS 0.004 0.001 HIS D 391 PHE 0.014 0.001 PHE B 119 TYR 0.015 0.001 TYR D 352 ARG 0.006 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 339 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.1510 (ptt) cc_final: 0.0188 (mtm) REVERT: A 433 TYR cc_start: -0.0058 (OUTLIER) cc_final: -0.1307 (m-80) REVERT: B 761 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8669 (mp) REVERT: B 886 MET cc_start: 0.8057 (mmp) cc_final: 0.7547 (mmt) REVERT: C 777 MET cc_start: 0.8177 (mtp) cc_final: 0.7953 (mtp) REVERT: D 571 GLN cc_start: 0.8275 (mt0) cc_final: 0.7969 (mt0) REVERT: D 582 GLU cc_start: 0.8137 (tp30) cc_final: 0.7892 (tp30) REVERT: D 777 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7752 (mtp) REVERT: E 647 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8644 (t) REVERT: E 891 MET cc_start: 0.1897 (mtm) cc_final: 0.0926 (tmm) REVERT: E 917 GLU cc_start: 0.5766 (tm-30) cc_final: 0.4954 (tt0) REVERT: F 152 MET cc_start: 0.4908 (mmt) cc_final: 0.4162 (tmm) REVERT: F 162 GLU cc_start: 0.5526 (mp0) cc_final: 0.5246 (tt0) REVERT: F 346 MET cc_start: 0.7563 (mmm) cc_final: 0.7359 (mmm) REVERT: F 676 ASP cc_start: 0.7104 (m-30) cc_final: 0.6793 (m-30) REVERT: F 891 MET cc_start: 0.3457 (mtm) cc_final: 0.1657 (mtm) outliers start: 43 outliers final: 13 residues processed: 364 average time/residue: 0.5315 time to fit residues: 323.6440 Evaluate side-chains 316 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 299 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 848 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.0670 chunk 328 optimal weight: 20.0000 chunk 226 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 293 optimal weight: 0.0970 chunk 438 optimal weight: 20.0000 chunk 463 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 chunk 415 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 887 ASN D 203 GLN D 542 GLN D 908 GLN E 203 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 40313 Z= 0.139 Angle : 0.475 8.843 54216 Z= 0.236 Chirality : 0.039 0.227 6057 Planarity : 0.003 0.032 6603 Dihedral : 14.586 89.726 7305 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.89 % Allowed : 9.34 % Favored : 89.77 % 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: 1.04 (0.12), residues: 4788 helix: 1.75 (0.10), residues: 2736 sheet: -0.44 (0.19), residues: 588 loop : -0.80 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 750 HIS 0.003 0.001 HIS B 495 PHE 0.013 0.001 PHE B 119 TYR 0.011 0.001 TYR C 691 ARG 0.005 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 335 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.1442 (ptt) cc_final: 0.0156 (mtm) REVERT: A 433 TYR cc_start: 0.0011 (OUTLIER) cc_final: -0.1147 (m-80) REVERT: A 803 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 902 ASP cc_start: 0.7938 (m-30) cc_final: 0.7727 (m-30) REVERT: B 592 MET cc_start: 0.8355 (ttm) cc_final: 0.7925 (ttp) REVERT: B 761 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8687 (mp) REVERT: B 795 MET cc_start: 0.8467 (mmm) cc_final: 0.8036 (mmp) REVERT: B 886 MET cc_start: 0.8031 (mmp) cc_final: 0.7543 (mmt) REVERT: C 791 MET cc_start: 0.7791 (ttp) cc_final: 0.7587 (ttm) REVERT: C 908 GLN cc_start: 0.7904 (tt0) cc_final: 0.7415 (tm-30) REVERT: D 571 GLN cc_start: 0.8267 (mt0) cc_final: 0.8010 (mt0) REVERT: D 582 GLU cc_start: 0.8104 (tp30) cc_final: 0.7846 (tp30) REVERT: E 258 MET cc_start: 0.4751 (pmm) cc_final: 0.4257 (pmm) REVERT: E 647 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8531 (t) REVERT: F 152 MET cc_start: 0.4928 (mmt) cc_final: 0.4265 (tmm) REVERT: F 676 ASP cc_start: 0.7034 (m-30) cc_final: 0.6798 (m-30) REVERT: F 891 MET cc_start: 0.3054 (mtm) cc_final: 0.1142 (mtm) outliers start: 35 outliers final: 17 residues processed: 354 average time/residue: 0.5018 time to fit residues: 299.0746 Evaluate side-chains 324 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 304 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 556 MET Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 848 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 345 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 395 optimal weight: 2.9990 chunk 320 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 416 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 792 ASN B 887 ASN C 792 ASN D 542 GLN D 908 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40313 Z= 0.222 Angle : 0.510 8.596 54216 Z= 0.252 Chirality : 0.040 0.205 6057 Planarity : 0.003 0.031 6603 Dihedral : 14.802 89.609 7305 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.99 % Allowed : 10.81 % Favored : 88.19 % 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: 1.14 (0.12), residues: 4788 helix: 1.82 (0.10), residues: 2748 sheet: -0.54 (0.20), residues: 594 loop : -0.69 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 309 HIS 0.005 0.001 HIS C 701 PHE 0.018 0.001 PHE A 510 TYR 0.013 0.001 TYR A 691 ARG 0.005 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 318 time to evaluate : 4.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 ASP cc_start: 0.7947 (m-30) cc_final: 0.7731 (m-30) REVERT: B 761 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 792 ASN cc_start: 0.8383 (m110) cc_final: 0.8162 (m110) REVERT: B 886 MET cc_start: 0.8056 (mmp) cc_final: 0.7615 (mmt) REVERT: C 791 MET cc_start: 0.7892 (ttp) cc_final: 0.7682 (ttm) REVERT: C 908 GLN cc_start: 0.7911 (tt0) cc_final: 0.7439 (tm-30) REVERT: D 571 GLN cc_start: 0.8263 (mt0) cc_final: 0.8009 (mt0) REVERT: E 258 MET cc_start: 0.4519 (pmm) cc_final: 0.4223 (pmm) REVERT: E 552 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8341 (pt) REVERT: E 599 ASP cc_start: 0.7628 (m-30) cc_final: 0.7115 (m-30) REVERT: E 647 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8835 (t) REVERT: E 912 THR cc_start: 0.8780 (m) cc_final: 0.8326 (p) REVERT: E 917 GLU cc_start: 0.5639 (tm-30) cc_final: 0.4804 (tt0) REVERT: F 152 MET cc_start: 0.4938 (mmt) cc_final: 0.4315 (tmm) REVERT: F 891 MET cc_start: 0.3151 (mtm) cc_final: 0.1412 (mtm) outliers start: 39 outliers final: 22 residues processed: 342 average time/residue: 0.5118 time to fit residues: 295.0710 Evaluate side-chains 323 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 2.9990 chunk 417 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 464 optimal weight: 0.7980 chunk 385 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN D 908 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 40313 Z= 0.301 Angle : 0.554 8.855 54216 Z= 0.271 Chirality : 0.042 0.227 6057 Planarity : 0.003 0.034 6603 Dihedral : 15.167 88.442 7303 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.30 % Allowed : 11.42 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.12), residues: 4788 helix: 1.67 (0.10), residues: 2748 sheet: -0.53 (0.21), residues: 516 loop : -0.78 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 309 HIS 0.006 0.001 HIS C 701 PHE 0.019 0.001 PHE A 510 TYR 0.015 0.001 TYR A 691 ARG 0.006 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 304 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 672 SER cc_start: 0.8347 (t) cc_final: 0.8000 (p) REVERT: B 761 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8781 (mp) REVERT: B 792 ASN cc_start: 0.8407 (m110) cc_final: 0.8086 (m110) REVERT: B 886 MET cc_start: 0.8058 (mmp) cc_final: 0.7674 (mmt) REVERT: C 777 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8110 (mtp) REVERT: C 908 GLN cc_start: 0.7917 (tt0) cc_final: 0.7414 (tm-30) REVERT: D 289 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7917 (m) REVERT: D 552 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8631 (pt) REVERT: D 571 GLN cc_start: 0.8305 (mt0) cc_final: 0.7978 (mt0) REVERT: D 848 ASN cc_start: 0.7701 (t0) cc_final: 0.7343 (t0) REVERT: E 258 MET cc_start: 0.4485 (pmm) cc_final: 0.3091 (ppp) REVERT: E 912 THR cc_start: 0.8823 (m) cc_final: 0.8342 (p) REVERT: E 917 GLU cc_start: 0.5707 (tm-30) cc_final: 0.4831 (tt0) REVERT: F 152 MET cc_start: 0.5198 (mmt) cc_final: 0.4437 (tmm) REVERT: F 891 MET cc_start: 0.3044 (mtm) cc_final: 0.1259 (mtm) outliers start: 51 outliers final: 28 residues processed: 336 average time/residue: 0.5468 time to fit residues: 316.0060 Evaluate side-chains 321 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 289 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 777 MET Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 899 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 264 optimal weight: 6.9990 chunk 339 optimal weight: 0.5980 chunk 262 optimal weight: 6.9990 chunk 390 optimal weight: 0.2980 chunk 259 optimal weight: 0.5980 chunk 462 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN B 291 ASN ** B 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN D 908 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 40313 Z= 0.158 Angle : 0.480 9.430 54216 Z= 0.237 Chirality : 0.040 0.251 6057 Planarity : 0.003 0.034 6603 Dihedral : 14.142 89.921 7303 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.12 % Allowed : 12.01 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4788 helix: 1.96 (0.10), residues: 2766 sheet: -0.64 (0.20), residues: 600 loop : -0.70 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 756 HIS 0.003 0.001 HIS F 686 PHE 0.018 0.001 PHE A 510 TYR 0.013 0.001 TYR C 691 ARG 0.003 0.000 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 314 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 MET cc_start: 0.7271 (mmp) cc_final: 0.7052 (mmt) REVERT: B 761 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 886 MET cc_start: 0.8007 (mmp) cc_final: 0.7634 (mmt) REVERT: C 118 MET cc_start: 0.4648 (OUTLIER) cc_final: 0.2525 (tpt) REVERT: C 405 MET cc_start: 0.4184 (ppp) cc_final: 0.2654 (tpt) REVERT: C 908 GLN cc_start: 0.7936 (tt0) cc_final: 0.7477 (tm-30) REVERT: D 552 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8551 (pt) REVERT: D 571 GLN cc_start: 0.8247 (mt0) cc_final: 0.7960 (mt0) REVERT: E 258 MET cc_start: 0.4479 (pmm) cc_final: 0.4202 (pmm) REVERT: E 912 THR cc_start: 0.8815 (m) cc_final: 0.8388 (p) REVERT: E 917 GLU cc_start: 0.5638 (tm-30) cc_final: 0.4762 (tt0) REVERT: F 152 MET cc_start: 0.5039 (mmt) cc_final: 0.4307 (tmm) REVERT: F 891 MET cc_start: 0.3096 (mtm) cc_final: 0.1392 (mtm) outliers start: 44 outliers final: 22 residues processed: 343 average time/residue: 0.5001 time to fit residues: 290.9346 Evaluate side-chains 317 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 876 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 276 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 90 optimal weight: 30.0000 chunk 89 optimal weight: 0.0980 chunk 294 optimal weight: 8.9990 chunk 315 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 363 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN ** B 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN D 542 GLN D 908 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40313 Z= 0.165 Angle : 0.486 9.122 54216 Z= 0.239 Chirality : 0.040 0.228 6057 Planarity : 0.003 0.034 6603 Dihedral : 13.832 89.991 7303 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.04 % Allowed : 12.37 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.12), residues: 4788 helix: 2.06 (0.10), residues: 2760 sheet: -0.65 (0.19), residues: 600 loop : -0.71 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 309 HIS 0.004 0.001 HIS B 701 PHE 0.019 0.001 PHE A 510 TYR 0.012 0.001 TYR A 691 ARG 0.003 0.000 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 851 ASP cc_start: 0.8485 (p0) cc_final: 0.8226 (p0) REVERT: B 258 MET cc_start: 0.5229 (mmt) cc_final: 0.4907 (mmp) REVERT: B 761 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8684 (mp) REVERT: B 886 MET cc_start: 0.8015 (mmp) cc_final: 0.7626 (mmt) REVERT: C 118 MET cc_start: 0.4646 (OUTLIER) cc_final: 0.2529 (tpt) REVERT: C 405 MET cc_start: 0.4118 (ppp) cc_final: 0.2648 (tpt) REVERT: C 631 MET cc_start: 0.8272 (mmm) cc_final: 0.7639 (tpp) REVERT: C 672 SER cc_start: 0.8659 (t) cc_final: 0.8225 (m) REVERT: C 908 GLN cc_start: 0.7930 (tt0) cc_final: 0.7464 (tm-30) REVERT: D 552 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8533 (pt) REVERT: D 571 GLN cc_start: 0.8283 (mt0) cc_final: 0.8005 (mt0) REVERT: E 258 MET cc_start: 0.4446 (pmm) cc_final: 0.3099 (ppp) REVERT: E 599 ASP cc_start: 0.7633 (m-30) cc_final: 0.7049 (m-30) REVERT: E 912 THR cc_start: 0.8732 (m) cc_final: 0.8341 (p) REVERT: E 917 GLU cc_start: 0.5607 (tm-30) cc_final: 0.4737 (tt0) REVERT: F 152 MET cc_start: 0.5044 (mmt) cc_final: 0.4415 (tmm) REVERT: F 891 MET cc_start: 0.2917 (mtm) cc_final: 0.1212 (mtm) outliers start: 41 outliers final: 30 residues processed: 336 average time/residue: 0.4902 time to fit residues: 280.9805 Evaluate side-chains 325 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 292 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 876 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 1.9990 chunk 443 optimal weight: 0.8980 chunk 404 optimal weight: 20.0000 chunk 431 optimal weight: 0.4980 chunk 259 optimal weight: 0.5980 chunk 187 optimal weight: 0.0570 chunk 338 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 389 optimal weight: 1.9990 chunk 407 optimal weight: 40.0000 chunk 429 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN ** B 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN D 908 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 40313 Z= 0.147 Angle : 0.473 9.548 54216 Z= 0.233 Chirality : 0.040 0.222 6057 Planarity : 0.003 0.033 6603 Dihedral : 13.241 89.024 7303 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.89 % Allowed : 12.52 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 4788 helix: 2.12 (0.10), residues: 2754 sheet: -0.59 (0.20), residues: 600 loop : -0.69 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 750 HIS 0.004 0.001 HIS B 686 PHE 0.018 0.001 PHE A 510 TYR 0.021 0.001 TYR B 352 ARG 0.004 0.000 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 314 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 792 ASN cc_start: 0.8190 (m-40) cc_final: 0.7951 (m110) REVERT: A 851 ASP cc_start: 0.8489 (p0) cc_final: 0.8231 (p0) REVERT: B 761 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8707 (mp) REVERT: B 886 MET cc_start: 0.8047 (mmp) cc_final: 0.7664 (mmt) REVERT: C 118 MET cc_start: 0.4661 (OUTLIER) cc_final: 0.2539 (tpt) REVERT: C 405 MET cc_start: 0.3999 (ppp) cc_final: 0.2588 (tpt) REVERT: C 632 THR cc_start: 0.8592 (p) cc_final: 0.8315 (p) REVERT: C 908 GLN cc_start: 0.7917 (tt0) cc_final: 0.7460 (tm-30) REVERT: D 552 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8533 (pt) REVERT: D 571 GLN cc_start: 0.8260 (mt0) cc_final: 0.8009 (mt0) REVERT: E 258 MET cc_start: 0.4719 (pmm) cc_final: 0.3373 (ppp) REVERT: E 405 MET cc_start: 0.2857 (ptm) cc_final: 0.2501 (ptm) REVERT: E 891 MET cc_start: 0.2492 (mtm) cc_final: 0.0754 (ttp) REVERT: E 902 ASP cc_start: 0.8253 (m-30) cc_final: 0.7749 (m-30) REVERT: E 912 THR cc_start: 0.8718 (m) cc_final: 0.8332 (p) REVERT: E 917 GLU cc_start: 0.5501 (tm-30) cc_final: 0.4653 (tt0) REVERT: F 152 MET cc_start: 0.4916 (mmt) cc_final: 0.4400 (tmm) REVERT: F 355 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7749 (mptt) REVERT: F 891 MET cc_start: 0.2831 (mtm) cc_final: 0.1194 (mtm) outliers start: 35 outliers final: 28 residues processed: 340 average time/residue: 0.5016 time to fit residues: 289.1861 Evaluate side-chains 330 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 299 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 632 THR Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 876 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 0.9980 chunk 455 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 316 optimal weight: 0.0980 chunk 478 optimal weight: 4.9990 chunk 440 optimal weight: 7.9990 chunk 380 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN ** B 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 HIS D 542 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 40313 Z= 0.252 Angle : 0.541 12.183 54216 Z= 0.264 Chirality : 0.042 0.261 6057 Planarity : 0.003 0.033 6603 Dihedral : 13.945 89.883 7303 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.02 % Allowed : 12.32 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4788 helix: 1.99 (0.10), residues: 2730 sheet: -0.67 (0.21), residues: 528 loop : -0.63 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 309 HIS 0.006 0.001 HIS B 701 PHE 0.020 0.001 PHE A 510 TYR 0.017 0.001 TYR B 352 ARG 0.003 0.000 ARG B 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 301 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 TYR cc_start: -0.0024 (OUTLIER) cc_final: -0.1372 (m-80) REVERT: A 632 THR cc_start: 0.8547 (p) cc_final: 0.8330 (p) REVERT: A 851 ASP cc_start: 0.8472 (p0) cc_final: 0.8186 (p0) REVERT: B 672 SER cc_start: 0.8387 (t) cc_final: 0.8064 (p) REVERT: B 761 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8786 (mp) REVERT: B 886 MET cc_start: 0.8031 (mmp) cc_final: 0.7666 (mmt) REVERT: C 118 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.2583 (tpt) REVERT: C 405 MET cc_start: 0.4042 (ppp) cc_final: 0.2695 (tpt) REVERT: C 538 ASP cc_start: 0.6657 (p0) cc_final: 0.6090 (m-30) REVERT: C 908 GLN cc_start: 0.7894 (tt0) cc_final: 0.7390 (tm-30) REVERT: D 552 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8596 (pt) REVERT: D 571 GLN cc_start: 0.8278 (mt0) cc_final: 0.7997 (mt0) REVERT: E 571 GLN cc_start: 0.7918 (mt0) cc_final: 0.7683 (mt0) REVERT: E 912 THR cc_start: 0.8775 (m) cc_final: 0.8352 (p) REVERT: F 152 MET cc_start: 0.4841 (mmt) cc_final: 0.4217 (tmm) REVERT: F 891 MET cc_start: 0.2798 (mtm) cc_final: 0.1137 (mtm) outliers start: 40 outliers final: 30 residues processed: 328 average time/residue: 0.4837 time to fit residues: 270.5438 Evaluate side-chains 330 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 632 THR Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.0970 chunk 405 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 381 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 391 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN B 792 ASN D 542 GLN E 227 GLN ** E 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.230544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.182323 restraints weight = 35853.661| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 4.21 r_work: 0.3869 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40313 Z= 0.171 Angle : 0.498 12.145 54216 Z= 0.244 Chirality : 0.040 0.236 6057 Planarity : 0.003 0.032 6603 Dihedral : 13.318 87.489 7303 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.92 % Allowed : 12.44 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.12), residues: 4788 helix: 2.04 (0.10), residues: 2754 sheet: -0.64 (0.21), residues: 528 loop : -0.63 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 750 HIS 0.003 0.001 HIS B 701 PHE 0.019 0.001 PHE A 510 TYR 0.017 0.001 TYR B 352 ARG 0.003 0.000 ARG D 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7838.66 seconds wall clock time: 145 minutes 6.44 seconds (8706.44 seconds total)