Starting phenix.real_space_refine on Tue Mar 12 21:55:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/03_2024/8i9u_35284_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/03_2024/8i9u_35284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/03_2024/8i9u_35284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/03_2024/8i9u_35284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/03_2024/8i9u_35284_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/03_2024/8i9u_35284_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.165 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 20 5.49 5 S 402 5.16 5 C 40830 2.51 5 N 11326 2.21 5 O 12563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C ASP 521": "OD1" <-> "OD2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E ASP 233": "OD1" <-> "OD2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E GLU 347": "OE1" <-> "OE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E ASP 531": "OD1" <-> "OD2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 482": "OE1" <-> "OE2" Residue "G PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H ASP 158": "OD1" <-> "OD2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H ASP 357": "OD1" <-> "OD2" Residue "H GLU 368": "OE1" <-> "OE2" Residue "H GLU 389": "OE1" <-> "OE2" Residue "H GLU 483": "OE1" <-> "OE2" Residue "H ASP 522": "OD1" <-> "OD2" Residue "I ASP 47": "OD1" <-> "OD2" Residue "I ASP 51": "OD1" <-> "OD2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 256": "OD1" <-> "OD2" Residue "I ASP 261": "OD1" <-> "OD2" Residue "I GLU 349": "OE1" <-> "OE2" Residue "I ASP 359": "OD1" <-> "OD2" Residue "I GLU 360": "OE1" <-> "OE2" Residue "I GLU 505": "OE1" <-> "OE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "J ASP 151": "OD1" <-> "OD2" Residue "J ASP 177": "OD1" <-> "OD2" Residue "J GLU 185": "OE1" <-> "OE2" Residue "J PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 277": "OE1" <-> "OE2" Residue "J GLU 280": "OE1" <-> "OE2" Residue "J GLU 339": "OE1" <-> "OE2" Residue "J ASP 403": "OD1" <-> "OD2" Residue "J TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 452": "OD1" <-> "OD2" Residue "J GLU 495": "OE1" <-> "OE2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "K PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K ARG 228": "NH1" <-> "NH2" Residue "K TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 280": "OE1" <-> "OE2" Residue "K GLU 358": "OE1" <-> "OE2" Residue "K ASP 521": "OD1" <-> "OD2" Residue "L ASP 73": "OD1" <-> "OD2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L ASP 204": "OD1" <-> "OD2" Residue "L ASP 220": "OD1" <-> "OD2" Residue "L ASP 261": "OD1" <-> "OD2" Residue "L ASP 268": "OD1" <-> "OD2" Residue "L TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 273": "OD1" <-> "OD2" Residue "L GLU 278": "OE1" <-> "OE2" Residue "L GLU 399": "OE1" <-> "OE2" Residue "L ARG 539": "NH1" <-> "NH2" Residue "M ASP 73": "OD1" <-> "OD2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M ASP 221": "OD1" <-> "OD2" Residue "M ASP 233": "OD1" <-> "OD2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 256": "OE1" <-> "OE2" Residue "M TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 329": "OE1" <-> "OE2" Residue "M GLU 347": "OE1" <-> "OE2" Residue "M GLU 351": "OE1" <-> "OE2" Residue "M ASP 404": "OD1" <-> "OD2" Residue "M TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 476": "OE1" <-> "OE2" Residue "M ASP 531": "OD1" <-> "OD2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "N GLU 192": "OE1" <-> "OE2" Residue "N GLU 201": "OE1" <-> "OE2" Residue "N PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 269": "OD1" <-> "OD2" Residue "N PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 338": "OD1" <-> "OD2" Residue "N GLU 461": "OE1" <-> "OE2" Residue "O PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "O TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 482": "OE1" <-> "OE2" Residue "O PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "P GLU 117": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P GLU 130": "OE1" <-> "OE2" Residue "P ASP 158": "OD1" <-> "OD2" Residue "P GLU 226": "OE1" <-> "OE2" Residue "P ASP 357": "OD1" <-> "OD2" Residue "P GLU 368": "OE1" <-> "OE2" Residue "P GLU 389": "OE1" <-> "OE2" Residue "P GLU 483": "OE1" <-> "OE2" Residue "P ASP 522": "OD1" <-> "OD2" Residue "Q PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 93": "OE1" <-> "OE2" Residue "Q ASP 101": "OD1" <-> "OD2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 160": "OD1" <-> "OD2" Residue "Q ASP 173": "OD1" <-> "OD2" Residue "Q GLU 200": "OE1" <-> "OE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 105": "OE1" <-> "OE2" Residue "R ARG 139": "NH1" <-> "NH2" Residue "R PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 171": "OE1" <-> "OE2" Residue "R ASP 192": "OD1" <-> "OD2" Residue "R GLU 195": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 65141 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3956 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 12, 'TRANS': 508} Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3755 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 8, 'TRANS': 490} Chain: "C" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3940 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 16, 'TRANS': 490} Chain: "D" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3880 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 14, 'TRANS': 499} Chain: "E" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3940 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 17, 'TRANS': 495} Chain: "F" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3958 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 13, 'TRANS': 502} Chain: "G" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3936 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 14, 'TRANS': 497} Chain: "H" Number of atoms: 3942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3942 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 13, 'TRANS': 503} Chain: "I" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3956 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 12, 'TRANS': 508} Chain: "J" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3755 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 8, 'TRANS': 490} Chain: "K" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3940 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 16, 'TRANS': 490} Chain: "L" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3880 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 14, 'TRANS': 499} Chain: "M" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3940 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 17, 'TRANS': 495} Chain: "N" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3958 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 13, 'TRANS': 502} Chain: "O" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3936 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 14, 'TRANS': 497} Chain: "P" Number of atoms: 3942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3942 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 13, 'TRANS': 503} Chain: "Q" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1133 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "R" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1124 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.82, per 1000 atoms: 0.44 Number of scatterers: 65141 At special positions: 0 Unit cell: (187.58, 200.01, 195.49, 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 402 16.00 P 20 15.00 O 12563 8.00 N 11326 7.00 C 40830 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.94 Conformation dependent library (CDL) restraints added in 11.3 seconds 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 283 helices and 52 sheets defined 43.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.85 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.629A pdb=" N SER A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.835A pdb=" N GLU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 removed outlier: 4.250A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 263 through 279 removed outlier: 4.550A pdb=" N GLU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.569A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.644A pdb=" N CYS A 385 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 436 through 445 removed outlier: 4.116A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 460 through 476 removed outlier: 3.710A pdb=" N GLU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 100 through 118 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 263 through 284 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.599A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'C' and resid 22 through 34 Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 75 through 90 Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 121 through 140 removed outlier: 3.693A pdb=" N ILE C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 261 through 282 removed outlier: 3.844A pdb=" N LEU C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C 269 " --> pdb=" O THR C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'C' and resid 317 through 325 Processing helix chain 'C' and resid 381 through 402 Processing helix chain 'C' and resid 414 through 429 Processing helix chain 'C' and resid 434 through 441 Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 490 through 493 No H-bonds generated for 'chain 'C' and resid 490 through 493' Processing helix chain 'C' and resid 500 through 517 Processing helix chain 'D' and resid 28 through 47 Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.524A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 161 through 170 Processing helix chain 'D' and resid 177 through 190 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 271 through 280 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 311 through 318 Processing helix chain 'D' and resid 330 through 339 Processing helix chain 'D' and resid 398 through 417 Processing helix chain 'D' and resid 427 through 442 Processing helix chain 'D' and resid 446 through 456 removed outlier: 3.545A pdb=" N TYR D 449 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 473 through 487 Processing helix chain 'D' and resid 513 through 531 removed outlier: 4.042A pdb=" N ALA D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 50 removed outlier: 4.025A pdb=" N THR E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 No H-bonds generated for 'chain 'E' and resid 76 through 79' Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.633A pdb=" N ASP E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 removed outlier: 3.762A pdb=" N GLU E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 removed outlier: 4.174A pdb=" N ILE E 166 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 197 removed outlier: 4.169A pdb=" N VAL E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 393 through 414 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 446 through 455 removed outlier: 3.661A pdb=" N ALA E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU E 455 " --> pdb=" O PHE E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 464 Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 72 through 84 removed outlier: 3.608A pdb=" N GLN F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 112 Processing helix chain 'F' and resid 116 through 137 Processing helix chain 'F' and resid 146 through 159 Processing helix chain 'F' and resid 167 through 179 removed outlier: 4.059A pdb=" N ALA F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 281 Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.640A pdb=" N ALA F 304 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 327 Processing helix chain 'F' and resid 383 through 403 Processing helix chain 'F' and resid 415 through 423 Processing helix chain 'F' and resid 431 through 442 removed outlier: 3.798A pdb=" N GLY F 436 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA F 439 " --> pdb=" O LEU F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 455 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 499 through 513 Processing helix chain 'G' and resid 19 through 35 removed outlier: 3.519A pdb=" N VAL G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 Processing helix chain 'G' and resid 74 through 89 Processing helix chain 'G' and resid 95 through 109 Processing helix chain 'G' and resid 118 through 139 removed outlier: 3.564A pdb=" N ILE G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE G 122 " --> pdb=" O GLN G 119 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG G 123 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 163 removed outlier: 4.382A pdb=" N LEU G 155 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU G 156 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 181 removed outlier: 3.520A pdb=" N PHE G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 227 No H-bonds generated for 'chain 'G' and resid 225 through 227' Processing helix chain 'G' and resid 261 through 282 removed outlier: 3.842A pdb=" N ILE G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 Processing helix chain 'G' and resid 316 through 326 Processing helix chain 'G' and resid 387 through 401 Processing helix chain 'G' and resid 413 through 426 removed outlier: 3.871A pdb=" N ARG G 425 " --> pdb=" O ARG G 421 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR G 426 " --> pdb=" O ASP G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 440 Processing helix chain 'G' and resid 445 through 452 Processing helix chain 'G' and resid 458 through 467 removed outlier: 3.904A pdb=" N ASN G 462 " --> pdb=" O THR G 458 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS G 463 " --> pdb=" O ASN G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 515 Processing helix chain 'H' and resid 31 through 41 removed outlier: 4.214A pdb=" N CYS H 36 " --> pdb=" O ASN H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 81 through 96 removed outlier: 4.237A pdb=" N ILE H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA H 89 " --> pdb=" O MET H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 121 removed outlier: 4.097A pdb=" N GLU H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 143 Processing helix chain 'H' and resid 158 through 168 removed outlier: 4.064A pdb=" N LEU H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 188 Processing helix chain 'H' and resid 262 through 285 Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'H' and resid 318 through 327 Processing helix chain 'H' and resid 385 through 399 Processing helix chain 'H' and resid 414 through 427 removed outlier: 3.988A pdb=" N GLU H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 454 removed outlier: 3.898A pdb=" N PHE H 445 " --> pdb=" O PHE H 441 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU H 446 " --> pdb=" O ALA H 442 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA H 447 " --> pdb=" O GLU H 443 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Proline residue: H 449 - end of helix Processing helix chain 'H' and resid 461 through 469 Processing helix chain 'H' and resid 482 through 484 No H-bonds generated for 'chain 'H' and resid 482 through 484' Processing helix chain 'H' and resid 501 through 520 Processing helix chain 'I' and resid 15 through 28 Processing helix chain 'I' and resid 33 through 35 No H-bonds generated for 'chain 'I' and resid 33 through 35' Processing helix chain 'I' and resid 60 through 63 No H-bonds generated for 'chain 'I' and resid 60 through 63' Processing helix chain 'I' and resid 70 through 85 removed outlier: 3.834A pdb=" N GLU I 85 " --> pdb=" O LEU I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 109 removed outlier: 4.247A pdb=" N GLU I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 132 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 165 through 177 Processing helix chain 'I' and resid 263 through 279 removed outlier: 4.696A pdb=" N GLU I 273 " --> pdb=" O ASP I 269 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG I 274 " --> pdb=" O ILE I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 300 Processing helix chain 'I' and resid 313 through 322 Processing helix chain 'I' and resid 382 through 386 removed outlier: 3.684A pdb=" N CYS I 385 " --> pdb=" O ASP I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 401 Processing helix chain 'I' and resid 416 through 430 Processing helix chain 'I' and resid 436 through 445 removed outlier: 4.088A pdb=" N LEU I 445 " --> pdb=" O PHE I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 455 Processing helix chain 'I' and resid 460 through 476 removed outlier: 3.722A pdb=" N GLU I 473 " --> pdb=" O ALA I 469 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA I 474 " --> pdb=" O PHE I 470 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN I 475 " --> pdb=" O HIS I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 526 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 79 through 95 Processing helix chain 'J' and resid 99 through 118 Processing helix chain 'J' and resid 123 through 143 Processing helix chain 'J' and resid 152 through 166 Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 263 through 284 Processing helix chain 'J' and resid 298 through 307 Processing helix chain 'J' and resid 319 through 326 Processing helix chain 'J' and resid 383 through 399 Processing helix chain 'J' and resid 413 through 424 Processing helix chain 'J' and resid 433 through 444 Processing helix chain 'J' and resid 446 through 454 removed outlier: 3.593A pdb=" N ALA J 454 " --> pdb=" O ILE J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 458 through 471 Processing helix chain 'J' and resid 488 through 491 No H-bonds generated for 'chain 'J' and resid 488 through 491' Processing helix chain 'J' and resid 498 through 515 Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 97 through 109 Processing helix chain 'K' and resid 121 through 140 removed outlier: 3.693A pdb=" N ILE K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 160 Processing helix chain 'K' and resid 169 through 183 Processing helix chain 'K' and resid 262 through 280 removed outlier: 3.519A pdb=" N LEU K 268 " --> pdb=" O PHE K 264 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU K 278 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU K 280 " --> pdb=" O GLN K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 306 Processing helix chain 'K' and resid 317 through 325 Processing helix chain 'K' and resid 381 through 402 Processing helix chain 'K' and resid 414 through 429 Processing helix chain 'K' and resid 434 through 441 Processing helix chain 'K' and resid 447 through 455 Processing helix chain 'K' and resid 461 through 469 Processing helix chain 'K' and resid 490 through 493 No H-bonds generated for 'chain 'K' and resid 490 through 493' Processing helix chain 'K' and resid 500 through 517 Processing helix chain 'L' and resid 28 through 47 Processing helix chain 'L' and resid 74 through 80 Processing helix chain 'L' and resid 86 through 101 Processing helix chain 'L' and resid 108 through 126 removed outlier: 3.519A pdb=" N LYS L 122 " --> pdb=" O ASP L 118 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 151 Processing helix chain 'L' and resid 161 through 170 Processing helix chain 'L' and resid 177 through 180 No H-bonds generated for 'chain 'L' and resid 177 through 180' Processing helix chain 'L' and resid 184 through 190 Processing helix chain 'L' and resid 271 through 280 Processing helix chain 'L' and resid 283 through 290 Processing helix chain 'L' and resid 311 through 316 Processing helix chain 'L' and resid 330 through 339 Processing helix chain 'L' and resid 398 through 417 Processing helix chain 'L' and resid 427 through 442 Processing helix chain 'L' and resid 446 through 456 removed outlier: 4.146A pdb=" N CYS L 450 " --> pdb=" O MET L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 469 Processing helix chain 'L' and resid 473 through 487 Processing helix chain 'L' and resid 513 through 531 removed outlier: 4.043A pdb=" N ALA L 518 " --> pdb=" O VAL L 514 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 50 removed outlier: 4.019A pdb=" N THR M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR M 50 " --> pdb=" O ASN M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 79 No H-bonds generated for 'chain 'M' and resid 76 through 79' Processing helix chain 'M' and resid 86 through 97 removed outlier: 3.585A pdb=" N LEU M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 126 removed outlier: 3.598A pdb=" N ASP M 125 " --> pdb=" O GLU M 121 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG M 126 " --> pdb=" O GLN M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 150 removed outlier: 3.764A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS M 150 " --> pdb=" O GLU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 172 removed outlier: 4.173A pdb=" N ILE M 166 " --> pdb=" O GLU M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 197 removed outlier: 4.169A pdb=" N VAL M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 295 Processing helix chain 'M' and resid 308 through 317 Processing helix chain 'M' and resid 328 through 334 Processing helix chain 'M' and resid 393 through 414 Processing helix chain 'M' and resid 424 through 435 Processing helix chain 'M' and resid 444 through 455 removed outlier: 3.706A pdb=" N ASP M 453 " --> pdb=" O ARG M 449 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA M 454 " --> pdb=" O ALA M 450 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU M 455 " --> pdb=" O PHE M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 458 through 464 Processing helix chain 'M' and resid 470 through 483 Processing helix chain 'M' and resid 510 through 529 Processing helix chain 'N' and resid 18 through 33 Processing helix chain 'N' and resid 61 through 65 Processing helix chain 'N' and resid 72 through 84 removed outlier: 3.579A pdb=" N GLN N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 112 Processing helix chain 'N' and resid 116 through 137 Processing helix chain 'N' and resid 146 through 157 Processing helix chain 'N' and resid 167 through 179 Processing helix chain 'N' and resid 253 through 281 Processing helix chain 'N' and resid 299 through 306 removed outlier: 3.632A pdb=" N ALA N 304 " --> pdb=" O PHE N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 318 through 327 Processing helix chain 'N' and resid 383 through 403 Processing helix chain 'N' and resid 415 through 423 Processing helix chain 'N' and resid 431 through 442 removed outlier: 3.800A pdb=" N GLY N 436 " --> pdb=" O ARG N 432 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA N 439 " --> pdb=" O LEU N 435 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 455 removed outlier: 4.288A pdb=" N ILE N 447 " --> pdb=" O LEU N 444 " (cutoff:3.500A) Proline residue: N 448 - end of helix removed outlier: 3.547A pdb=" N SER N 455 " --> pdb=" O ALA N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 499 through 513 Processing helix chain 'O' and resid 19 through 35 removed outlier: 3.519A pdb=" N VAL O 31 " --> pdb=" O SER O 27 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 74 through 89 Processing helix chain 'O' and resid 95 through 109 Processing helix chain 'O' and resid 118 through 139 removed outlier: 3.561A pdb=" N ILE O 121 " --> pdb=" O PRO O 118 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE O 122 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG O 123 " --> pdb=" O ILE O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 163 Processing helix chain 'O' and resid 170 through 181 Processing helix chain 'O' and resid 225 through 227 No H-bonds generated for 'chain 'O' and resid 225 through 227' Processing helix chain 'O' and resid 261 through 282 removed outlier: 3.822A pdb=" N ILE O 273 " --> pdb=" O ALA O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 305 Processing helix chain 'O' and resid 316 through 326 Processing helix chain 'O' and resid 387 through 401 Processing helix chain 'O' and resid 413 through 426 removed outlier: 3.864A pdb=" N ARG O 425 " --> pdb=" O ARG O 421 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR O 426 " --> pdb=" O ASP O 422 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 442 removed outlier: 3.517A pdb=" N LEU O 442 " --> pdb=" O TYR O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 452 Processing helix chain 'O' and resid 458 through 469 removed outlier: 3.882A pdb=" N ASN O 462 " --> pdb=" O THR O 458 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS O 463 " --> pdb=" O ASN O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 498 through 515 Processing helix chain 'P' and resid 27 through 29 No H-bonds generated for 'chain 'P' and resid 27 through 29' Processing helix chain 'P' and resid 31 through 41 removed outlier: 3.743A pdb=" N ALA P 35 " --> pdb=" O ARG P 31 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N CYS P 36 " --> pdb=" O ASN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 75 Processing helix chain 'P' and resid 81 through 96 removed outlier: 4.244A pdb=" N ILE P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL P 87 " --> pdb=" O ALA P 83 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET P 88 " --> pdb=" O LYS P 84 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA P 89 " --> pdb=" O MET P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 121 removed outlier: 4.071A pdb=" N GLU P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU P 118 " --> pdb=" O LEU P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 143 Processing helix chain 'P' and resid 158 through 168 removed outlier: 4.064A pdb=" N LEU P 163 " --> pdb=" O GLU P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 Processing helix chain 'P' and resid 212 through 214 No H-bonds generated for 'chain 'P' and resid 212 through 214' Processing helix chain 'P' and resid 262 through 285 Processing helix chain 'P' and resid 299 through 307 Processing helix chain 'P' and resid 318 through 327 Processing helix chain 'P' and resid 385 through 399 Processing helix chain 'P' and resid 414 through 427 removed outlier: 3.987A pdb=" N GLU P 418 " --> pdb=" O ALA P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 435 through 454 removed outlier: 3.899A pdb=" N PHE P 445 " --> pdb=" O PHE P 441 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU P 446 " --> pdb=" O ALA P 442 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA P 447 " --> pdb=" O GLU P 443 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE P 448 " --> pdb=" O ALA P 444 " (cutoff:3.500A) Proline residue: P 449 - end of helix Processing helix chain 'P' and resid 461 through 469 Processing helix chain 'P' and resid 482 through 484 No H-bonds generated for 'chain 'P' and resid 482 through 484' Processing helix chain 'P' and resid 501 through 520 Processing helix chain 'Q' and resid 100 through 108 removed outlier: 5.040A pdb=" N VAL Q 106 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 140 removed outlier: 3.671A pdb=" N GLY Q 136 " --> pdb=" O GLN Q 132 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG Q 139 " --> pdb=" O SER Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 201 Processing helix chain 'Q' and resid 219 through 231 removed outlier: 3.679A pdb=" N SER Q 223 " --> pdb=" O VAL Q 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 108 removed outlier: 3.511A pdb=" N THR R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 138 Processing helix chain 'R' and resid 181 through 183 No H-bonds generated for 'chain 'R' and resid 181 through 183' Processing helix chain 'R' and resid 191 through 198 Processing helix chain 'R' and resid 220 through 231 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= B, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.681A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 289 through 291 removed outlier: 5.892A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 48 through 51 Processing sheet with id= E, first strand: chain 'C' and resid 213 through 215 Processing sheet with id= F, first strand: chain 'C' and resid 407 through 409 Processing sheet with id= G, first strand: chain 'C' and resid 478 through 480 Processing sheet with id= H, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= I, first strand: chain 'D' and resid 222 through 224 removed outlier: 4.277A pdb=" N GLU D 222 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 389 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= K, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= L, first strand: chain 'E' and resid 210 through 215 removed outlier: 3.764A pdb=" N ILE E 385 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU E 212 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE E 387 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS E 214 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 229 through 231 Processing sheet with id= N, first strand: chain 'E' and resid 248 through 250 removed outlier: 6.223A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 45 through 47 Processing sheet with id= P, first strand: chain 'F' and resid 204 through 207 Processing sheet with id= Q, first strand: chain 'F' and resid 210 through 212 Processing sheet with id= R, first strand: chain 'F' and resid 345 through 347 removed outlier: 7.016A pdb=" N GLY F 288 " --> pdb=" O TYR F 229 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU F 231 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL F 290 " --> pdb=" O LEU F 231 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 47 through 50 Processing sheet with id= T, first strand: chain 'G' and resid 209 through 211 Processing sheet with id= U, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.547A pdb=" N GLU G 356 " --> pdb=" O ILE G 353 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 405 through 407 Processing sheet with id= W, first strand: chain 'H' and resid 54 through 56 removed outlier: 3.894A pdb=" N PHE H 64 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 202 through 208 removed outlier: 6.756A pdb=" N SER H 373 " --> pdb=" O ARG H 203 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS H 205 " --> pdb=" O SER H 373 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE H 375 " --> pdb=" O CYS H 205 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE H 207 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU H 377 " --> pdb=" O ILE H 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'H' and resid 349 through 355 removed outlier: 3.972A pdb=" N SER H 349 " --> pdb=" O LYS H 364 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 43 through 46 Processing sheet with id= AA, first strand: chain 'I' and resid 350 through 352 removed outlier: 3.669A pdb=" N GLU I 350 " --> pdb=" O LYS I 365 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 289 through 291 removed outlier: 5.886A pdb=" N MET J 310 " --> pdb=" O PHE J 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'K' and resid 48 through 51 Processing sheet with id= AD, first strand: chain 'K' and resid 213 through 215 Processing sheet with id= AE, first strand: chain 'K' and resid 407 through 409 Processing sheet with id= AF, first strand: chain 'K' and resid 478 through 480 Processing sheet with id= AG, first strand: chain 'L' and resid 59 through 62 Processing sheet with id= AH, first strand: chain 'L' and resid 222 through 224 removed outlier: 4.259A pdb=" N GLU L 222 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL L 389 " --> pdb=" O GLU L 222 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 227 through 229 Processing sheet with id= AJ, first strand: chain 'M' and resid 59 through 62 Processing sheet with id= AK, first strand: chain 'M' and resid 210 through 215 removed outlier: 3.764A pdb=" N ILE M 385 " --> pdb=" O LYS M 210 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU M 212 " --> pdb=" O ILE M 385 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE M 387 " --> pdb=" O GLU M 212 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS M 214 " --> pdb=" O ILE M 387 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY M 389 " --> pdb=" O LYS M 214 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 229 through 231 Processing sheet with id= AM, first strand: chain 'M' and resid 248 through 250 removed outlier: 6.220A pdb=" N LEU M 299 " --> pdb=" O ALA M 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'N' and resid 45 through 47 removed outlier: 3.715A pdb=" N LYS N 45 " --> pdb=" O THR N 57 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR N 57 " --> pdb=" O LYS N 45 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 203 through 207 removed outlier: 4.215A pdb=" N ASP N 203 " --> pdb=" O LYS N 377 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 210 through 212 Processing sheet with id= AQ, first strand: chain 'N' and resid 345 through 347 removed outlier: 6.801A pdb=" N GLY N 288 " --> pdb=" O TYR N 229 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU N 231 " --> pdb=" O GLY N 288 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL N 290 " --> pdb=" O LEU N 231 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 47 through 50 Processing sheet with id= AS, first strand: chain 'O' and resid 208 through 211 Processing sheet with id= AT, first strand: chain 'O' and resid 347 through 353 removed outlier: 3.513A pdb=" N GLU O 356 " --> pdb=" O ILE O 353 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'O' and resid 405 through 407 Processing sheet with id= AV, first strand: chain 'P' and resid 54 through 56 removed outlier: 3.874A pdb=" N PHE P 64 " --> pdb=" O VAL P 56 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'P' and resid 202 through 208 removed outlier: 6.757A pdb=" N SER P 373 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS P 205 " --> pdb=" O SER P 373 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE P 375 " --> pdb=" O CYS P 205 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE P 207 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU P 377 " --> pdb=" O ILE P 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'P' and resid 349 through 355 removed outlier: 3.972A pdb=" N SER P 349 " --> pdb=" O LYS P 364 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 145 through 150 Processing sheet with id= AZ, first strand: chain 'R' and resid 145 through 148 2624 hydrogen bonds defined for protein. 7503 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: 21.22 Time building geometry restraints manager: 23.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 21969 1.34 - 1.46: 12064 1.46 - 1.58: 31186 1.58 - 1.70: 30 1.70 - 1.81: 664 Bond restraints: 65913 Sorted by residual: bond pdb=" CA ASP K 281 " pdb=" C ASP K 281 " ideal model delta sigma weight residual 1.533 1.524 0.009 5.60e-03 3.19e+04 2.85e+00 bond pdb=" CA LEU C 241 " pdb=" C LEU C 241 " ideal model delta sigma weight residual 1.531 1.523 0.007 5.40e-03 3.43e+04 1.73e+00 bond pdb=" N LEU E 443 " pdb=" CA LEU E 443 " ideal model delta sigma weight residual 1.458 1.468 -0.010 9.00e-03 1.23e+04 1.18e+00 bond pdb=" C SER K 380 " pdb=" O SER K 380 " ideal model delta sigma weight residual 1.234 1.244 -0.010 1.00e-02 1.00e+04 1.09e+00 bond pdb=" C SER C 380 " pdb=" O SER C 380 " ideal model delta sigma weight residual 1.234 1.244 -0.010 1.00e-02 1.00e+04 1.04e+00 ... (remaining 65908 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.88: 1828 107.88 - 114.96: 41784 114.96 - 122.03: 32147 122.03 - 129.11: 12958 129.11 - 136.18: 276 Bond angle restraints: 88993 Sorted by residual: angle pdb=" N ILE I 149 " pdb=" CA ILE I 149 " pdb=" C ILE I 149 " ideal model delta sigma weight residual 113.71 109.30 4.41 9.50e-01 1.11e+00 2.15e+01 angle pdb=" C ASP K 281 " pdb=" CA ASP K 281 " pdb=" CB ASP K 281 " ideal model delta sigma weight residual 117.07 110.55 6.52 1.44e+00 4.82e-01 2.05e+01 angle pdb=" CA ASP K 281 " pdb=" C ASP K 281 " pdb=" O ASP K 281 " ideal model delta sigma weight residual 117.94 120.50 -2.56 5.80e-01 2.97e+00 1.94e+01 angle pdb=" N VAL E 271 " pdb=" CA VAL E 271 " pdb=" C VAL E 271 " ideal model delta sigma weight residual 113.53 109.31 4.22 9.80e-01 1.04e+00 1.85e+01 angle pdb=" C LEU C 241 " pdb=" CA LEU C 241 " pdb=" CB LEU C 241 " ideal model delta sigma weight residual 116.53 110.37 6.16 1.47e+00 4.63e-01 1.76e+01 ... (remaining 88988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.65: 38642 28.65 - 57.31: 2002 57.31 - 85.96: 147 85.96 - 114.61: 13 114.61 - 143.26: 15 Dihedral angle restraints: 40819 sinusoidal: 16404 harmonic: 24415 Sorted by residual: dihedral pdb=" C5' ADP L 601 " pdb=" O5' ADP L 601 " pdb=" PA ADP L 601 " pdb=" O2A ADP L 601 " ideal model delta sinusoidal sigma weight residual 300.00 156.74 143.26 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O2A ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PA ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sinusoidal sigma weight residual -60.00 69.36 -129.36 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 68.60 -128.60 1 2.00e+01 2.50e-03 3.90e+01 ... (remaining 40816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 6928 0.026 - 0.052: 2150 0.052 - 0.077: 814 0.077 - 0.103: 518 0.103 - 0.129: 239 Chirality restraints: 10649 Sorted by residual: chirality pdb=" CA ILE L 300 " pdb=" N ILE L 300 " pdb=" C ILE L 300 " pdb=" CB ILE L 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE D 300 " pdb=" N ILE D 300 " pdb=" C ILE D 300 " pdb=" CB ILE D 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE D 422 " pdb=" N ILE D 422 " pdb=" C ILE D 422 " pdb=" CB ILE D 422 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 10646 not shown) Planarity restraints: 11369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 256 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO E 257 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 257 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 257 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 256 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO M 257 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO M 257 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO M 257 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 445 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO G 446 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO G 446 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO G 446 " 0.015 5.00e-02 4.00e+02 ... (remaining 11366 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 12643 2.78 - 3.31: 57144 3.31 - 3.84: 99389 3.84 - 4.37: 100752 4.37 - 4.90: 186400 Nonbonded interactions: 456328 Sorted by model distance: nonbonded pdb=" O VAL H 355 " pdb=" OG1 THR H 358 " model vdw 2.250 2.440 nonbonded pdb=" O VAL P 355 " pdb=" OG1 THR P 358 " model vdw 2.251 2.440 nonbonded pdb=" OD2 ASP C 132 " pdb=" OH TYR C 437 " model vdw 2.262 2.440 nonbonded pdb=" OD2 ASP K 132 " pdb=" OH TYR K 437 " model vdw 2.263 2.440 nonbonded pdb=" OE2 GLU H 17 " pdb=" OG SER H 23 " model vdw 2.265 2.440 ... (remaining 456323 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 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = (chain 'Q' and resid 91 through 232) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 9.670 Check model and map are aligned: 0.780 Set scattering table: 0.490 Process input model: 140.010 Find NCS groups from input model: 5.750 Set up NCS constraints: 0.570 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: 0.020 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 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 : 0.001 0.037 65913 Z= 0.092 Angle : 0.420 6.572 88993 Z= 0.239 Chirality : 0.037 0.129 10649 Planarity : 0.002 0.036 11369 Dihedral : 15.884 143.263 25005 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.10 % Favored : 87.16 % Rotamer: Outliers : 1.78 % Allowed : 16.62 % Favored : 81.61 % 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: -2.67 (0.08), residues: 8447 helix: -0.04 (0.08), residues: 3968 sheet: -1.56 (0.21), residues: 533 loop : -3.83 (0.07), residues: 3946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP Q 114 HIS 0.001 0.000 HIS J 174 PHE 0.004 0.000 PHE H 64 TYR 0.005 0.000 TYR F 239 ARG 0.001 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 996 time to evaluate : 5.552 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 161 ILE cc_start: 0.1741 (OUTLIER) cc_final: 0.1419 (mp) REVERT: A 225 MET cc_start: 0.1068 (mtp) cc_final: -0.1218 (mmt) REVERT: A 256 ASP cc_start: 0.3205 (OUTLIER) cc_final: 0.1546 (t0) REVERT: B 48 MET cc_start: 0.7945 (mmt) cc_final: 0.7620 (mmt) REVERT: B 452 ASP cc_start: 0.7280 (t70) cc_final: 0.7073 (m-30) REVERT: C 374 ILE cc_start: 0.6668 (tt) cc_final: 0.6301 (tt) REVERT: E 239 MET cc_start: 0.1171 (ttm) cc_final: 0.0843 (ttp) REVERT: G 487 ASN cc_start: 0.7131 (m-40) cc_final: 0.6904 (m-40) REVERT: I 145 ARG cc_start: 0.3365 (mmt180) cc_final: 0.1812 (ttt180) REVERT: I 225 MET cc_start: -0.1132 (mtp) cc_final: -0.1771 (ptm) REVERT: I 344 MET cc_start: 0.2576 (ptt) cc_final: 0.2288 (mmm) REVERT: J 205 LEU cc_start: -0.1294 (OUTLIER) cc_final: -0.1962 (mt) REVERT: J 275 MET cc_start: -0.3037 (ptp) cc_final: -0.4077 (tpt) REVERT: K 49 MET cc_start: 0.8072 (ttm) cc_final: 0.7774 (ttm) REVERT: K 105 MET cc_start: 0.7557 (mtt) cc_final: 0.7207 (mtt) REVERT: L 57 MET cc_start: 0.6347 (mmp) cc_final: 0.5293 (mmm) REVERT: L 60 MET cc_start: 0.5239 (ttm) cc_final: 0.5013 (ttp) REVERT: L 219 ASP cc_start: 0.4068 (OUTLIER) cc_final: 0.3541 (m-30) REVERT: M 239 MET cc_start: 0.3183 (ttm) cc_final: 0.2810 (ttm) REVERT: Q 119 LEU cc_start: 0.3307 (OUTLIER) cc_final: 0.2537 (tt) REVERT: R 204 ILE cc_start: 0.5228 (OUTLIER) cc_final: 0.4915 (tp) outliers start: 126 outliers final: 24 residues processed: 1108 average time/residue: 0.5826 time to fit residues: 1091.1892 Evaluate side-chains 601 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 571 time to evaluate : 5.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 508 CYS Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain I residue 409 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 508 CYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 1.9990 chunk 636 optimal weight: 40.0000 chunk 353 optimal weight: 8.9990 chunk 217 optimal weight: 0.5980 chunk 429 optimal weight: 0.0270 chunk 340 optimal weight: 0.7980 chunk 658 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 chunk 400 optimal weight: 0.9990 chunk 490 optimal weight: 1.9990 chunk 762 optimal weight: 0.0970 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 320 ASN D 368 ASN D 502 ASN E 46 ASN E 264 HIS E 290 GLN E 503 GLN E 516 GLN F 23 ASN F 65 HIS F 84 GLN F 161 HIS F 386 GLN G 25 ASN G 119 GLN G 432 GLN G 462 ASN G 501 ASN H 58 ASN H 80 HIS H 172 GLN H 185 GLN H 201 ASN ** H 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN H 359 GLN H 365 HIS I 20 GLN ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 GLN K 320 ASN K 526 HIS L 368 ASN L 472 ASN M 46 ASN M 147 HIS M 182 HIS M 403 HIS M 503 GLN M 516 GLN N 23 ASN N 68 GLN N 467 GLN N 497 ASN O 25 ASN O 119 GLN O 432 GLN O 462 ASN O 501 ASN P 309 ASN P 359 GLN P 365 HIS R 132 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 65913 Z= 0.126 Angle : 0.495 12.938 88993 Z= 0.236 Chirality : 0.039 0.173 10649 Planarity : 0.003 0.074 11369 Dihedral : 5.808 137.086 9154 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.78 % Favored : 93.06 % Rotamer: Outliers : 1.71 % Allowed : 19.41 % Favored : 78.89 % 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: -1.61 (0.09), residues: 8447 helix: 1.03 (0.09), residues: 3951 sheet: -0.95 (0.22), residues: 545 loop : -3.51 (0.08), residues: 3951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 485 HIS 0.015 0.001 HIS H 365 PHE 0.006 0.001 PHE B 179 TYR 0.016 0.001 TYR A 190 ARG 0.010 0.000 ARG P 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 577 time to evaluate : 5.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7448 (tppt) cc_final: 0.7196 (mmmt) REVERT: A 161 ILE cc_start: 0.1564 (OUTLIER) cc_final: 0.1310 (mp) REVERT: A 225 MET cc_start: 0.1258 (mtp) cc_final: -0.1157 (mmt) REVERT: B 48 MET cc_start: 0.7873 (mmt) cc_final: 0.7660 (mmm) REVERT: E 239 MET cc_start: 0.1406 (ttm) cc_final: 0.1016 (ttp) REVERT: G 323 MET cc_start: 0.3394 (tmm) cc_final: 0.2963 (tmm) REVERT: H 300 MET cc_start: 0.4574 (mmm) cc_final: 0.4184 (mmm) REVERT: H 378 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5430 (mtp180) REVERT: I 145 ARG cc_start: 0.3426 (mmt180) cc_final: 0.2120 (ttt-90) REVERT: I 306 MET cc_start: 0.3470 (mmt) cc_final: 0.1240 (ptp) REVERT: J 95 VAL cc_start: 0.4450 (m) cc_final: 0.4244 (t) REVERT: J 275 MET cc_start: -0.2945 (ptp) cc_final: -0.4078 (tpt) REVERT: K 105 MET cc_start: 0.7588 (mtt) cc_final: 0.7205 (mtt) REVERT: L 471 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7385 (mt) REVERT: M 60 MET cc_start: 0.4512 (ppp) cc_final: 0.2775 (ttp) REVERT: M 239 MET cc_start: 0.3158 (ttm) cc_final: 0.2833 (ttm) REVERT: O 227 MET cc_start: 0.1338 (mmm) cc_final: 0.0098 (mtm) REVERT: O 394 MET cc_start: 0.5129 (mmt) cc_final: 0.4853 (mpp) outliers start: 121 outliers final: 47 residues processed: 670 average time/residue: 0.6036 time to fit residues: 715.0688 Evaluate side-chains 566 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 516 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 65 HIS Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 227 MET Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 507 ILE Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 494 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 184 MET Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 468 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 0.2980 chunk 236 optimal weight: 30.0000 chunk 634 optimal weight: 5.9990 chunk 519 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 764 optimal weight: 1.9990 chunk 825 optimal weight: 8.9990 chunk 680 optimal weight: 10.0000 chunk 757 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 613 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 301 GLN D 406 HIS E 184 GLN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 84 GLN F 386 GLN F 497 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS G 171 GLN G 448 GLN ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 HIS ** H 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN H 471 HIS ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 GLN K 115 GLN K 157 ASN K 226 HIS K 470 HIS M 72 ASN M 290 GLN M 505 HIS N 503 GLN O 117 HIS O 201 GLN O 241 ASN ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 472 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 65913 Z= 0.387 Angle : 0.802 16.946 88993 Z= 0.398 Chirality : 0.048 0.253 10649 Planarity : 0.005 0.070 11369 Dihedral : 6.743 179.828 9124 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.26 % Favored : 91.63 % Rotamer: Outliers : 3.74 % Allowed : 19.58 % Favored : 76.69 % 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: -1.70 (0.09), residues: 8447 helix: 0.82 (0.08), residues: 3895 sheet: -0.76 (0.22), residues: 525 loop : -3.37 (0.08), residues: 4027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP O 493 HIS 0.040 0.002 HIS F 65 PHE 0.042 0.002 PHE O 125 TYR 0.034 0.002 TYR A 422 ARG 0.010 0.001 ARG N 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 567 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8023 (t) REVERT: B 359 LEU cc_start: 0.1569 (OUTLIER) cc_final: 0.1268 (mm) REVERT: C 59 MET cc_start: 0.8522 (ptp) cc_final: 0.8227 (ptp) REVERT: C 349 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4749 (pt) REVERT: D 323 MET cc_start: 0.2273 (ttp) cc_final: 0.1904 (ttm) REVERT: D 349 ASP cc_start: 0.0688 (OUTLIER) cc_final: 0.0210 (p0) REVERT: E 65 ASP cc_start: 0.4340 (OUTLIER) cc_final: 0.4107 (m-30) REVERT: E 170 LYS cc_start: 0.2824 (mmtm) cc_final: 0.2614 (mmtt) REVERT: E 239 MET cc_start: 0.1486 (ttm) cc_final: 0.1049 (ttp) REVERT: E 501 MET cc_start: 0.6855 (mmp) cc_final: 0.6185 (mmt) REVERT: F 414 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8302 (t) REVERT: F 510 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8484 (t) REVERT: G 382 MET cc_start: 0.1569 (mmp) cc_final: 0.0684 (mmt) REVERT: H 208 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5814 (mm) REVERT: H 300 MET cc_start: 0.4516 (mmm) cc_final: 0.4165 (mmm) REVERT: H 492 MET cc_start: 0.7757 (mtt) cc_final: 0.6939 (mtt) REVERT: I 306 MET cc_start: 0.3292 (mmt) cc_final: 0.1719 (ptm) REVERT: J 53 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7610 (tt) REVERT: J 275 MET cc_start: -0.2564 (ptp) cc_final: -0.4062 (tpt) REVERT: J 436 MET cc_start: 0.8170 (mtt) cc_final: 0.7623 (mtm) REVERT: L 260 MET cc_start: 0.3093 (ptp) cc_final: 0.2619 (ptm) REVERT: L 374 LEU cc_start: 0.2362 (OUTLIER) cc_final: 0.2121 (pp) REVERT: L 532 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7825 (mt) REVERT: M 60 MET cc_start: 0.5335 (ppp) cc_final: 0.4483 (ttp) REVERT: M 239 MET cc_start: 0.3899 (ttm) cc_final: 0.3621 (ttm) REVERT: M 371 MET cc_start: 0.3522 (OUTLIER) cc_final: 0.3125 (ttt) REVERT: N 487 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7391 (ppp) REVERT: O 81 ASP cc_start: 0.7277 (m-30) cc_final: 0.7059 (m-30) REVERT: O 497 MET cc_start: 0.7579 (tpp) cc_final: 0.7317 (mmm) REVERT: R 97 ILE cc_start: 0.3438 (OUTLIER) cc_final: 0.2971 (tt) outliers start: 265 outliers final: 114 residues processed: 778 average time/residue: 0.5498 time to fit residues: 756.8428 Evaluate side-chains 604 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 476 time to evaluate : 5.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 440 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain N residue 494 VAL Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 182 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 1.9990 chunk 574 optimal weight: 10.0000 chunk 396 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 364 optimal weight: 0.8980 chunk 513 optimal weight: 2.9990 chunk 766 optimal weight: 5.9990 chunk 811 optimal weight: 0.8980 chunk 400 optimal weight: 0.7980 chunk 726 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS D 482 ASN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN I 110 GLN ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN M 505 HIS N 68 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 65913 Z= 0.132 Angle : 0.531 11.393 88993 Z= 0.258 Chirality : 0.040 0.211 10649 Planarity : 0.003 0.062 11369 Dihedral : 5.692 176.519 9121 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 2.21 % Allowed : 21.45 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.09), residues: 8447 helix: 1.42 (0.09), residues: 3894 sheet: -0.74 (0.23), residues: 492 loop : -3.18 (0.08), residues: 4061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 485 HIS 0.010 0.001 HIS D 406 PHE 0.011 0.001 PHE N 289 TYR 0.015 0.001 TYR H 501 ARG 0.005 0.000 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 516 time to evaluate : 5.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 480 MET cc_start: 0.8151 (mmm) cc_final: 0.7771 (mmp) REVERT: C 117 MET cc_start: 0.2134 (mtm) cc_final: 0.1841 (mtm) REVERT: C 336 GLU cc_start: 0.3009 (OUTLIER) cc_final: 0.2141 (tt0) REVERT: D 323 MET cc_start: 0.2027 (ttp) cc_final: 0.1635 (ttm) REVERT: D 406 HIS cc_start: 0.4772 (OUTLIER) cc_final: 0.4159 (t-90) REVERT: E 208 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3872 (tt) REVERT: E 220 GLU cc_start: 0.3174 (tp30) cc_final: 0.2955 (tp30) REVERT: E 239 MET cc_start: 0.1310 (ttm) cc_final: 0.0224 (tpt) REVERT: E 501 MET cc_start: 0.6772 (mmp) cc_final: 0.6084 (mmt) REVERT: F 108 LEU cc_start: 0.7261 (tt) cc_final: 0.6997 (tp) REVERT: G 174 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4461 (m-80) REVERT: G 382 MET cc_start: 0.1522 (mmp) cc_final: 0.0502 (mmt) REVERT: H 300 MET cc_start: 0.4443 (mmm) cc_final: 0.4143 (mmm) REVERT: H 344 MET cc_start: 0.3264 (mmm) cc_final: 0.3053 (mmm) REVERT: I 145 ARG cc_start: 0.3349 (mmt180) cc_final: 0.2026 (ttt-90) REVERT: I 306 MET cc_start: 0.3281 (mmt) cc_final: 0.1712 (ptm) REVERT: J 38 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7493 (mt) REVERT: J 275 MET cc_start: -0.2729 (ptp) cc_final: -0.3888 (tpt) REVERT: J 436 MET cc_start: 0.7868 (mtt) cc_final: 0.7599 (mtm) REVERT: L 260 MET cc_start: 0.3103 (ptp) cc_final: 0.2670 (ptm) REVERT: M 60 MET cc_start: 0.5201 (ppp) cc_final: 0.4877 (ptm) REVERT: M 239 MET cc_start: 0.3868 (ttm) cc_final: 0.3475 (mtp) REVERT: M 342 VAL cc_start: 0.0900 (OUTLIER) cc_final: 0.0563 (t) REVERT: M 371 MET cc_start: 0.3165 (OUTLIER) cc_final: 0.2628 (ttt) REVERT: O 497 MET cc_start: 0.7332 (tpp) cc_final: 0.7100 (mmm) REVERT: P 14 MET cc_start: 0.5462 (ppp) cc_final: 0.5172 (ppp) REVERT: P 492 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7066 (mtt) outliers start: 157 outliers final: 82 residues processed: 639 average time/residue: 0.5502 time to fit residues: 616.8465 Evaluate side-chains 556 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 466 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 511 ILE Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 184 MET Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 0.1980 chunk 460 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 604 optimal weight: 0.9980 chunk 335 optimal weight: 0.2980 chunk 692 optimal weight: 2.9990 chunk 561 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 414 optimal weight: 0.6980 chunk 728 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN P 471 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 65913 Z= 0.119 Angle : 0.496 9.666 88993 Z= 0.238 Chirality : 0.039 0.187 10649 Planarity : 0.003 0.067 11369 Dihedral : 5.181 164.363 9119 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 2.13 % Allowed : 21.61 % Favored : 76.26 % 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: -0.83 (0.09), residues: 8447 helix: 1.74 (0.09), residues: 3897 sheet: -0.64 (0.24), residues: 500 loop : -3.08 (0.08), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.025 0.001 HIS K 470 PHE 0.009 0.001 PHE F 362 TYR 0.014 0.001 TYR H 501 ARG 0.006 0.000 ARG I 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 477 time to evaluate : 5.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 480 MET cc_start: 0.8157 (mmm) cc_final: 0.7627 (mmp) REVERT: C 117 MET cc_start: 0.1598 (mtm) cc_final: 0.1362 (mtm) REVERT: D 323 MET cc_start: 0.1862 (ttp) cc_final: 0.1463 (ttm) REVERT: D 406 HIS cc_start: 0.4892 (OUTLIER) cc_final: 0.4531 (t-90) REVERT: E 208 LEU cc_start: 0.4109 (OUTLIER) cc_final: 0.3822 (tt) REVERT: E 239 MET cc_start: 0.1416 (ttm) cc_final: 0.0320 (tpt) REVERT: G 174 PHE cc_start: 0.5048 (OUTLIER) cc_final: 0.4375 (m-80) REVERT: G 382 MET cc_start: 0.1509 (mmp) cc_final: 0.0533 (mmt) REVERT: H 300 MET cc_start: 0.4425 (mmm) cc_final: 0.4160 (mmm) REVERT: I 145 ARG cc_start: 0.3373 (mmt180) cc_final: 0.2063 (ttt-90) REVERT: I 171 MET cc_start: 0.5234 (OUTLIER) cc_final: 0.4554 (mpp) REVERT: I 206 MET cc_start: 0.1092 (ttt) cc_final: 0.0888 (ttt) REVERT: I 306 MET cc_start: 0.3266 (mmt) cc_final: 0.1685 (ptm) REVERT: J 38 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7482 (mt) REVERT: J 275 MET cc_start: -0.2715 (ptp) cc_final: -0.3930 (tpt) REVERT: J 436 MET cc_start: 0.7868 (mtt) cc_final: 0.7589 (mtm) REVERT: K 105 MET cc_start: 0.8300 (mtt) cc_final: 0.7845 (mtt) REVERT: L 260 MET cc_start: 0.3128 (ptp) cc_final: 0.2707 (ptm) REVERT: M 60 MET cc_start: 0.5189 (ppp) cc_final: 0.4946 (ptm) REVERT: M 239 MET cc_start: 0.3861 (ttm) cc_final: 0.3297 (mtp) REVERT: M 342 VAL cc_start: 0.0852 (OUTLIER) cc_final: 0.0533 (t) REVERT: M 371 MET cc_start: 0.3212 (OUTLIER) cc_final: 0.2675 (ttt) REVERT: O 497 MET cc_start: 0.7289 (tpp) cc_final: 0.7070 (mmm) REVERT: P 14 MET cc_start: 0.5260 (ppp) cc_final: 0.4997 (ppp) REVERT: P 169 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6609 (mtp) REVERT: P 492 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.6884 (mtt) outliers start: 151 outliers final: 100 residues processed: 592 average time/residue: 0.6025 time to fit residues: 633.2258 Evaluate side-chains 570 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 461 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 468 MET Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 184 MET Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 8.9990 chunk 731 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 476 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 812 optimal weight: 0.1980 chunk 674 optimal weight: 0.9990 chunk 376 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 426 optimal weight: 0.2980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN D 406 HIS ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN P 50 ASN P 172 GLN ** P 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 65913 Z= 0.173 Angle : 0.534 13.136 88993 Z= 0.257 Chirality : 0.040 0.193 10649 Planarity : 0.003 0.068 11369 Dihedral : 5.066 150.129 9119 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.13 % Favored : 93.77 % Rotamer: Outliers : 2.62 % Allowed : 21.69 % Favored : 75.69 % 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: -0.75 (0.09), residues: 8447 helix: 1.77 (0.09), residues: 3905 sheet: -0.61 (0.24), residues: 494 loop : -3.00 (0.08), residues: 4048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 493 HIS 0.033 0.001 HIS K 470 PHE 0.015 0.001 PHE P 103 TYR 0.017 0.001 TYR C 437 ARG 0.007 0.000 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 487 time to evaluate : 5.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 MET cc_start: 0.1452 (mtm) cc_final: 0.1181 (mtm) REVERT: C 336 GLU cc_start: 0.3230 (OUTLIER) cc_final: 0.2237 (tt0) REVERT: D 323 MET cc_start: 0.1931 (ttp) cc_final: 0.1567 (ttm) REVERT: D 406 HIS cc_start: 0.4653 (OUTLIER) cc_final: 0.3870 (t-90) REVERT: E 59 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7269 (mttp) REVERT: E 208 LEU cc_start: 0.4186 (OUTLIER) cc_final: 0.3965 (tt) REVERT: E 220 GLU cc_start: 0.3361 (tp30) cc_final: 0.3022 (tp30) REVERT: E 239 MET cc_start: 0.1770 (ttm) cc_final: 0.0495 (tpt) REVERT: G 174 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4481 (m-80) REVERT: G 382 MET cc_start: 0.1513 (mmp) cc_final: 0.0631 (mmt) REVERT: G 442 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8499 (mp) REVERT: H 300 MET cc_start: 0.4470 (mmm) cc_final: 0.4222 (mmm) REVERT: I 145 ARG cc_start: 0.3350 (mmt180) cc_final: 0.2029 (ttt-90) REVERT: I 171 MET cc_start: 0.5372 (OUTLIER) cc_final: 0.4689 (mpp) REVERT: I 306 MET cc_start: 0.3237 (mmt) cc_final: 0.1698 (ptm) REVERT: I 344 MET cc_start: 0.2212 (mtm) cc_final: 0.1380 (mmm) REVERT: J 38 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7442 (mt) REVERT: J 275 MET cc_start: -0.2720 (ptp) cc_final: -0.4191 (tpt) REVERT: J 436 MET cc_start: 0.7953 (mtt) cc_final: 0.7570 (mtm) REVERT: L 260 MET cc_start: 0.3153 (ptp) cc_final: 0.2756 (ptm) REVERT: M 239 MET cc_start: 0.4013 (ttm) cc_final: 0.3461 (mtp) REVERT: M 307 ASP cc_start: 0.1013 (OUTLIER) cc_final: 0.0802 (p0) REVERT: M 342 VAL cc_start: 0.1309 (OUTLIER) cc_final: 0.0996 (t) REVERT: M 371 MET cc_start: 0.3373 (OUTLIER) cc_final: 0.2826 (ttt) REVERT: M 393 MET cc_start: 0.5038 (pmm) cc_final: 0.4739 (mpp) REVERT: O 497 MET cc_start: 0.7430 (tpp) cc_final: 0.7205 (mmm) REVERT: P 14 MET cc_start: 0.5394 (ppp) cc_final: 0.5076 (ppp) REVERT: P 16 LYS cc_start: 0.7977 (mmmm) cc_final: 0.7727 (mmmm) REVERT: P 85 MET cc_start: 0.8312 (mmm) cc_final: 0.7859 (mtp) outliers start: 186 outliers final: 133 residues processed: 629 average time/residue: 0.5382 time to fit residues: 595.4177 Evaluate side-chains 613 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 469 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 50 ASN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 481 ASP Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 463 optimal weight: 0.7980 chunk 593 optimal weight: 6.9990 chunk 459 optimal weight: 3.9990 chunk 684 optimal weight: 8.9990 chunk 453 optimal weight: 0.5980 chunk 809 optimal weight: 0.7980 chunk 506 optimal weight: 4.9990 chunk 493 optimal weight: 20.0000 chunk 373 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN O 282 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 65913 Z= 0.147 Angle : 0.514 12.297 88993 Z= 0.248 Chirality : 0.040 0.177 10649 Planarity : 0.003 0.068 11369 Dihedral : 4.952 147.419 9116 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.92 % Favored : 93.97 % Rotamer: Outliers : 2.54 % Allowed : 21.92 % Favored : 75.55 % 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: -0.67 (0.09), residues: 8447 helix: 1.81 (0.09), residues: 3916 sheet: -0.82 (0.23), residues: 542 loop : -2.94 (0.08), residues: 3989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.011 0.001 HIS K 470 PHE 0.010 0.001 PHE N 362 TYR 0.014 0.001 TYR C 437 ARG 0.005 0.000 ARG I 443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 485 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 480 MET cc_start: 0.8161 (mmm) cc_final: 0.7614 (mmp) REVERT: C 117 MET cc_start: 0.1442 (mtm) cc_final: 0.1197 (mtm) REVERT: C 336 GLU cc_start: 0.3505 (OUTLIER) cc_final: 0.2421 (tt0) REVERT: D 323 MET cc_start: 0.1881 (ttp) cc_final: 0.1524 (ttm) REVERT: D 406 HIS cc_start: 0.4788 (OUTLIER) cc_final: 0.4266 (t70) REVERT: E 59 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7312 (ttmm) REVERT: E 208 LEU cc_start: 0.4167 (OUTLIER) cc_final: 0.3955 (tt) REVERT: E 239 MET cc_start: 0.1776 (ttm) cc_final: 0.0501 (tpt) REVERT: F 510 VAL cc_start: 0.8488 (t) cc_final: 0.8252 (t) REVERT: G 174 PHE cc_start: 0.5185 (OUTLIER) cc_final: 0.4547 (m-80) REVERT: H 300 MET cc_start: 0.4457 (mmm) cc_final: 0.4218 (mmm) REVERT: I 145 ARG cc_start: 0.3314 (mmt180) cc_final: 0.2012 (ttt-90) REVERT: I 171 MET cc_start: 0.5354 (OUTLIER) cc_final: 0.4689 (mpp) REVERT: I 344 MET cc_start: 0.2299 (mtm) cc_final: 0.1422 (mmm) REVERT: J 38 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7405 (mt) REVERT: J 275 MET cc_start: -0.2741 (ptp) cc_final: -0.4197 (tpt) REVERT: J 310 MET cc_start: 0.1257 (tmm) cc_final: 0.1027 (mtt) REVERT: J 436 MET cc_start: 0.7936 (mtt) cc_final: 0.7595 (mtm) REVERT: L 151 MET cc_start: 0.4515 (tmm) cc_final: 0.4169 (ttp) REVERT: L 260 MET cc_start: 0.3220 (ptp) cc_final: 0.2850 (ptm) REVERT: M 59 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6867 (mttp) REVERT: M 239 MET cc_start: 0.4035 (ttm) cc_final: 0.3480 (mtp) REVERT: M 342 VAL cc_start: 0.1318 (OUTLIER) cc_final: 0.1016 (t) REVERT: M 371 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.3106 (ttt) REVERT: M 393 MET cc_start: 0.4999 (pmm) cc_final: 0.4669 (mpp) REVERT: O 497 MET cc_start: 0.7450 (tpp) cc_final: 0.7234 (mmm) REVERT: P 14 MET cc_start: 0.5264 (ppp) cc_final: 0.4962 (ppp) REVERT: P 85 MET cc_start: 0.8297 (mmm) cc_final: 0.7950 (mtp) REVERT: P 492 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7216 (mtt) outliers start: 180 outliers final: 136 residues processed: 625 average time/residue: 0.5410 time to fit residues: 599.1417 Evaluate side-chains 617 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 470 time to evaluate : 5.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 271 GLN Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 417 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 481 ASP Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 0.9980 chunk 323 optimal weight: 40.0000 chunk 483 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 156 optimal weight: 0.3980 chunk 514 optimal weight: 0.0170 chunk 551 optimal weight: 5.9990 chunk 400 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 636 optimal weight: 8.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 65913 Z= 0.124 Angle : 0.498 11.409 88993 Z= 0.238 Chirality : 0.039 0.244 10649 Planarity : 0.003 0.070 11369 Dihedral : 4.791 141.674 9115 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.56 % Favored : 94.33 % Rotamer: Outliers : 2.48 % Allowed : 22.06 % Favored : 75.46 % 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: -0.54 (0.09), residues: 8447 helix: 1.93 (0.09), residues: 3920 sheet: -0.84 (0.22), residues: 583 loop : -2.88 (0.08), residues: 3944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.034 0.001 HIS K 470 PHE 0.012 0.001 PHE N 362 TYR 0.014 0.001 TYR F 229 ARG 0.005 0.000 ARG K 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 485 time to evaluate : 5.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.4309 (ptp) cc_final: 0.3864 (ptt) REVERT: B 480 MET cc_start: 0.8145 (mmm) cc_final: 0.7891 (mmm) REVERT: C 516 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7986 (mt) REVERT: D 323 MET cc_start: 0.1821 (ttp) cc_final: 0.1473 (ttm) REVERT: D 406 HIS cc_start: 0.4879 (OUTLIER) cc_final: 0.4401 (t70) REVERT: E 59 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7519 (ttmm) REVERT: E 208 LEU cc_start: 0.4122 (OUTLIER) cc_final: 0.3912 (tt) REVERT: E 239 MET cc_start: 0.1807 (ttm) cc_final: 0.0535 (tpt) REVERT: G 174 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.4407 (m-80) REVERT: G 382 MET cc_start: 0.1576 (mmp) cc_final: -0.0035 (mmt) REVERT: I 145 ARG cc_start: 0.3286 (mmt180) cc_final: 0.1990 (ttt-90) REVERT: I 171 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4694 (mpp) REVERT: I 306 MET cc_start: 0.3090 (mmt) cc_final: 0.1550 (ttt) REVERT: I 344 MET cc_start: 0.2234 (mtm) cc_final: 0.1419 (mmp) REVERT: I 430 MET cc_start: 0.5988 (tpp) cc_final: 0.5552 (tpt) REVERT: J 38 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7345 (mt) REVERT: J 275 MET cc_start: -0.2772 (ptp) cc_final: -0.4206 (tpt) REVERT: J 310 MET cc_start: 0.1254 (tmm) cc_final: 0.1021 (mtt) REVERT: J 436 MET cc_start: 0.7847 (mtt) cc_final: 0.7598 (mtm) REVERT: K 105 MET cc_start: 0.8248 (mtt) cc_final: 0.7832 (mtt) REVERT: L 151 MET cc_start: 0.4535 (tmm) cc_final: 0.4191 (ttp) REVERT: L 260 MET cc_start: 0.3035 (ptp) cc_final: 0.2731 (ptm) REVERT: M 59 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6989 (mttp) REVERT: M 239 MET cc_start: 0.4035 (ttm) cc_final: 0.3489 (mtp) REVERT: M 342 VAL cc_start: 0.1235 (OUTLIER) cc_final: 0.1011 (t) REVERT: M 371 MET cc_start: 0.3438 (OUTLIER) cc_final: 0.3043 (ttt) REVERT: M 393 MET cc_start: 0.5025 (pmm) cc_final: 0.4712 (mpp) REVERT: O 497 MET cc_start: 0.7407 (tpp) cc_final: 0.7204 (mmm) REVERT: P 14 MET cc_start: 0.5041 (ppp) cc_final: 0.4680 (ppp) REVERT: P 85 MET cc_start: 0.8246 (mmm) cc_final: 0.7940 (mtp) REVERT: P 492 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7056 (mtt) outliers start: 176 outliers final: 127 residues processed: 621 average time/residue: 0.5712 time to fit residues: 629.4732 Evaluate side-chains 611 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 473 time to evaluate : 5.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 291 ILE Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 271 GLN Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 417 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 481 ASP Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain P residue 500 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 10.0000 chunk 775 optimal weight: 7.9990 chunk 707 optimal weight: 0.5980 chunk 754 optimal weight: 2.9990 chunk 454 optimal weight: 0.0370 chunk 328 optimal weight: 0.3980 chunk 592 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 681 optimal weight: 0.4980 chunk 713 optimal weight: 2.9990 chunk 751 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS G 241 ASN ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN O 73 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 65913 Z= 0.111 Angle : 0.493 11.434 88993 Z= 0.234 Chirality : 0.039 0.195 10649 Planarity : 0.003 0.068 11369 Dihedral : 4.650 137.744 9115 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.66 % Rotamer: Outliers : 2.02 % Allowed : 22.51 % Favored : 75.48 % 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: -0.39 (0.09), residues: 8447 helix: 2.04 (0.09), residues: 3924 sheet: -0.54 (0.23), residues: 535 loop : -2.80 (0.08), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.008 0.000 HIS B 178 PHE 0.013 0.001 PHE F 362 TYR 0.014 0.001 TYR F 229 ARG 0.005 0.000 ARG I 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 482 time to evaluate : 5.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.4328 (ptp) cc_final: 0.3882 (ptt) REVERT: B 480 MET cc_start: 0.8155 (mmm) cc_final: 0.7924 (mmm) REVERT: C 229 MET cc_start: 0.1738 (mmp) cc_final: 0.1460 (mmp) REVERT: C 516 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7801 (mt) REVERT: D 323 MET cc_start: 0.1942 (ttp) cc_final: 0.1567 (ttm) REVERT: E 208 LEU cc_start: 0.4093 (OUTLIER) cc_final: 0.3880 (tt) REVERT: E 239 MET cc_start: 0.1799 (ttm) cc_final: 0.0533 (tpt) REVERT: F 221 MET cc_start: 0.3990 (OUTLIER) cc_final: 0.3455 (mpp) REVERT: G 174 PHE cc_start: 0.5169 (OUTLIER) cc_final: 0.4289 (m-80) REVERT: G 323 MET cc_start: 0.3352 (tmm) cc_final: 0.2935 (tmm) REVERT: G 382 MET cc_start: 0.1588 (mmp) cc_final: 0.0011 (mmt) REVERT: H 300 MET cc_start: 0.2590 (mmm) cc_final: 0.2367 (mmm) REVERT: I 145 ARG cc_start: 0.3198 (mmt180) cc_final: 0.1951 (ttt-90) REVERT: I 171 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.4726 (mpp) REVERT: I 306 MET cc_start: 0.2921 (mmt) cc_final: 0.1376 (ttt) REVERT: I 344 MET cc_start: 0.2097 (mtm) cc_final: 0.1396 (mmm) REVERT: J 38 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7311 (mt) REVERT: J 48 MET cc_start: 0.8057 (mmt) cc_final: 0.7680 (mmm) REVERT: J 275 MET cc_start: -0.2800 (ptp) cc_final: -0.4210 (tpt) REVERT: J 436 MET cc_start: 0.7772 (mtt) cc_final: 0.7517 (mtm) REVERT: L 260 MET cc_start: 0.3134 (ptp) cc_final: 0.2785 (ptm) REVERT: M 59 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6928 (mttp) REVERT: M 239 MET cc_start: 0.4027 (ttm) cc_final: 0.3478 (mtp) REVERT: M 371 MET cc_start: 0.3507 (OUTLIER) cc_final: 0.3128 (ttt) REVERT: M 393 MET cc_start: 0.5023 (pmm) cc_final: 0.4726 (mpp) REVERT: P 14 MET cc_start: 0.4828 (ppp) cc_final: 0.4414 (ppp) REVERT: P 85 MET cc_start: 0.8162 (mmm) cc_final: 0.7922 (mtp) REVERT: P 492 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.6791 (mtt) outliers start: 143 outliers final: 112 residues processed: 593 average time/residue: 0.5423 time to fit residues: 569.2609 Evaluate side-chains 591 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 470 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 291 ILE Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 271 GLN Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 417 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 459 LYS Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain P residue 500 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 20.0000 chunk 797 optimal weight: 5.9990 chunk 486 optimal weight: 9.9990 chunk 378 optimal weight: 40.0000 chunk 554 optimal weight: 0.6980 chunk 836 optimal weight: 3.9990 chunk 770 optimal weight: 2.9990 chunk 666 optimal weight: 6.9990 chunk 69 optimal weight: 50.0000 chunk 514 optimal weight: 0.9980 chunk 408 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 HIS K 470 HIS M 290 GLN P 50 ASN P 346 HIS ** P 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 65913 Z= 0.204 Angle : 0.585 14.058 88993 Z= 0.282 Chirality : 0.041 0.246 10649 Planarity : 0.004 0.068 11369 Dihedral : 4.987 145.904 9115 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.57 % Rotamer: Outliers : 2.21 % Allowed : 22.31 % Favored : 75.48 % 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: -0.55 (0.09), residues: 8447 helix: 1.86 (0.09), residues: 3908 sheet: -0.62 (0.22), residues: 583 loop : -2.83 (0.09), residues: 3956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 493 HIS 0.032 0.001 HIS K 470 PHE 0.022 0.001 PHE P 103 TYR 0.020 0.001 TYR C 437 ARG 0.005 0.000 ARG K 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 471 time to evaluate : 5.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.4398 (ptp) cc_final: 0.3953 (ptt) REVERT: B 480 MET cc_start: 0.8238 (mmm) cc_final: 0.7711 (mmp) REVERT: C 229 MET cc_start: 0.1720 (mmp) cc_final: 0.1511 (mmp) REVERT: C 336 GLU cc_start: 0.3406 (OUTLIER) cc_final: 0.2345 (tt0) REVERT: E 59 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7283 (mttp) REVERT: E 170 LYS cc_start: 0.3278 (mmtm) cc_final: 0.3053 (mmtt) REVERT: E 208 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3963 (tt) REVERT: E 239 MET cc_start: 0.1834 (ttm) cc_final: 0.0580 (tpt) REVERT: F 510 VAL cc_start: 0.8671 (t) cc_final: 0.8453 (t) REVERT: G 174 PHE cc_start: 0.5230 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: G 382 MET cc_start: 0.1449 (mmp) cc_final: -0.0055 (mmt) REVERT: I 145 ARG cc_start: 0.3314 (mmt180) cc_final: 0.2057 (ttt-90) REVERT: I 167 PHE cc_start: 0.3955 (OUTLIER) cc_final: 0.3133 (m-80) REVERT: I 171 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4858 (mpp) REVERT: I 306 MET cc_start: 0.2980 (mmt) cc_final: 0.1382 (ttt) REVERT: I 344 MET cc_start: 0.2214 (mtm) cc_final: 0.1405 (mmm) REVERT: J 38 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7435 (mt) REVERT: J 275 MET cc_start: -0.2857 (ptp) cc_final: -0.3964 (tpt) REVERT: J 436 MET cc_start: 0.8018 (mtt) cc_final: 0.7497 (mtm) REVERT: L 260 MET cc_start: 0.3175 (ptp) cc_final: 0.2883 (ptm) REVERT: M 59 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.6907 (mttm) REVERT: M 239 MET cc_start: 0.4053 (ttm) cc_final: 0.3477 (mtp) REVERT: M 371 MET cc_start: 0.3693 (OUTLIER) cc_final: 0.3253 (ttt) REVERT: P 14 MET cc_start: 0.5197 (ppp) cc_final: 0.4839 (ppp) REVERT: P 85 MET cc_start: 0.8234 (mmm) cc_final: 0.8012 (mtp) outliers start: 157 outliers final: 127 residues processed: 599 average time/residue: 0.5501 time to fit residues: 584.7739 Evaluate side-chains 598 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 462 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 271 GLN Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 533 ASP Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 417 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 459 LYS Chi-restraints excluded: chain P residue 481 ASP Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain P residue 500 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 8.9990 chunk 709 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 614 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 667 optimal weight: 0.7980 chunk 279 optimal weight: 7.9990 chunk 685 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 HIS ** H 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN ** P 477 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 = 0.4765 r_free = 0.4765 target = 0.251805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.207943 restraints weight = 85717.978| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.64 r_work: 0.3958 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 65913 Z= 0.149 Angle : 0.529 11.851 88993 Z= 0.254 Chirality : 0.040 0.226 10649 Planarity : 0.003 0.062 11369 Dihedral : 4.868 141.842 9115 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 2.02 % Allowed : 22.58 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.09), residues: 8447 helix: 1.93 (0.09), residues: 3920 sheet: -0.65 (0.23), residues: 546 loop : -2.77 (0.09), residues: 3981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 474 HIS 0.007 0.001 HIS E 403 PHE 0.013 0.001 PHE M 306 TYR 0.014 0.001 TYR F 229 ARG 0.005 0.000 ARG C 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12781.14 seconds wall clock time: 226 minutes 18.14 seconds (13578.14 seconds total)