Starting phenix.real_space_refine on Sun Apr 14 11:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o00_0564/04_2024/6o00_0564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o00_0564/04_2024/6o00_0564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o00_0564/04_2024/6o00_0564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o00_0564/04_2024/6o00_0564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o00_0564/04_2024/6o00_0564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o00_0564/04_2024/6o00_0564.pdb" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 S 102 5.16 5 C 10398 2.51 5 N 2532 2.21 5 O 2724 1.98 5 H 15714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 364": "OD1" <-> "OD2" Residue "F ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31470 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Time building chain proxies: 13.95, per 1000 atoms: 0.44 Number of scatterers: 31470 At special positions: 0 Unit cell: (109.888, 103.36, 131.648, 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 102 16.00 O 2724 8.00 N 2532 7.00 C 10398 6.00 H 15714 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.65 Conformation dependent library (CDL) restraints added in 2.7 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 76.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 47 removed outlier: 3.744A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 3.788A pdb=" N LEU A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 4.209A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 287 removed outlier: 3.805A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 346 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.857A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.744A pdb=" N THR B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 146 removed outlier: 3.506A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 3.788A pdb=" N LEU B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.513A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 287 removed outlier: 3.805A pdb=" N ILE B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 384 through 395 removed outlier: 4.311A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.745A pdb=" N THR C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 3.787A pdb=" N LEU C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 256 removed outlier: 3.735A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 287 removed outlier: 3.805A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 21 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 removed outlier: 3.745A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 3.788A pdb=" N LEU D 131 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 287 removed outlier: 3.806A pdb=" N ILE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 21 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 removed outlier: 3.744A pdb=" N THR E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.789A pdb=" N LEU E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 4.209A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 287 removed outlier: 3.806A pdb=" N ILE E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 346 Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 384 through 395 removed outlier: 4.313A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 394 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 408 Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.857A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 47 removed outlier: 3.745A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 3.788A pdb=" N LEU F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 140 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.513A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 256 removed outlier: 3.735A pdb=" N LYS F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 255 " --> pdb=" O ARG F 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 287 removed outlier: 3.806A pdb=" N ILE F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 346 Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU F 358 " --> pdb=" O GLU F 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 394 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AB1, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 61 984 hydrogen bonds defined for protein. 2898 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: 11.29 Time building geometry restraints manager: 25.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 15687 0.99 - 1.20: 12 1.20 - 1.40: 6939 1.40 - 1.61: 9138 1.61 - 1.81: 144 Bond restraints: 31920 Sorted by residual: bond pdb=" ND2 ASN A 408 " pdb="HD22 ASN A 408 " ideal model delta sigma weight residual 0.860 0.788 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" ND2 ASN D 408 " pdb="HD22 ASN D 408 " ideal model delta sigma weight residual 0.860 0.788 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB ASN E 408 " pdb=" CG ASN E 408 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" CB ASN C 408 " pdb=" CG ASN C 408 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.63e+00 bond pdb=" CB ASN A 408 " pdb=" CG ASN A 408 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.62e+00 ... (remaining 31915 not shown) Histogram of bond angle deviations from ideal: 96.73 - 105.04: 271 105.04 - 113.36: 36738 113.36 - 121.67: 15020 121.67 - 129.98: 5379 129.98 - 138.30: 156 Bond angle restraints: 57564 Sorted by residual: angle pdb=" CG ASN F 408 " pdb=" ND2 ASN F 408 " pdb="HD21 ASN F 408 " ideal model delta sigma weight residual 120.00 97.96 22.04 3.00e+00 1.11e-01 5.40e+01 angle pdb=" CG ASN F 408 " pdb=" ND2 ASN F 408 " pdb="HD22 ASN F 408 " ideal model delta sigma weight residual 120.00 138.30 -18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" CG ASN D 408 " pdb=" ND2 ASN D 408 " pdb="HD21 ASN D 408 " ideal model delta sigma weight residual 120.00 131.91 -11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CG ASN A 408 " pdb=" ND2 ASN A 408 " pdb="HD21 ASN A 408 " ideal model delta sigma weight residual 120.00 131.86 -11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CG GLU E 236 " pdb=" CB GLU E 236 " pdb=" HB2 GLU E 236 " ideal model delta sigma weight residual 108.00 96.73 11.27 3.00e+00 1.11e-01 1.41e+01 ... (remaining 57559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 13097 16.11 - 32.23: 1470 32.23 - 48.34: 381 48.34 - 64.45: 142 64.45 - 80.56: 12 Dihedral angle restraints: 15102 sinusoidal: 7830 harmonic: 7272 Sorted by residual: dihedral pdb=" CA CYS F 139 " pdb=" C CYS F 139 " pdb=" N SER F 140 " pdb=" CA SER F 140 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS E 139 " pdb=" C CYS E 139 " pdb=" N SER E 140 " pdb=" CA SER E 140 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS C 139 " pdb=" C CYS C 139 " pdb=" N SER C 140 " pdb=" CA SER C 140 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 15099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1416 0.028 - 0.055: 660 0.055 - 0.083: 229 0.083 - 0.110: 73 0.110 - 0.138: 28 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA VAL D 368 " pdb=" N VAL D 368 " pdb=" C VAL D 368 " pdb=" CB VAL D 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL B 368 " pdb=" N VAL B 368 " pdb=" C VAL B 368 " pdb=" CB VAL B 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL A 368 " pdb=" N VAL A 368 " pdb=" C VAL A 368 " pdb=" CB VAL A 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2403 not shown) Planarity restraints: 4458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 408 " 0.000 2.00e-02 2.50e+03 3.08e-02 1.42e+01 pdb=" CG ASN F 408 " 0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN F 408 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 408 " 0.061 2.00e-02 2.50e+03 pdb="HD21 ASN F 408 " -0.007 2.00e-02 2.50e+03 pdb="HD22 ASN F 408 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 408 " 0.023 2.00e-02 2.50e+03 2.39e-02 8.57e+00 pdb=" CG ASN D 408 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 408 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN D 408 " -0.031 2.00e-02 2.50e+03 pdb="HD21 ASN D 408 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN D 408 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 408 " 0.023 2.00e-02 2.50e+03 2.38e-02 8.52e+00 pdb=" CG ASN A 408 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 408 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 408 " -0.031 2.00e-02 2.50e+03 pdb="HD21 ASN A 408 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN A 408 " -0.012 2.00e-02 2.50e+03 ... (remaining 4455 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 4775 2.27 - 2.85: 71485 2.85 - 3.44: 82478 3.44 - 4.02: 110366 4.02 - 4.60: 165791 Nonbonded interactions: 434895 Sorted by model distance: nonbonded pdb="HE21 GLN E 46 " pdb=" OD2 ASP E 50 " model vdw 1.688 1.850 nonbonded pdb="HE21 GLN F 46 " pdb=" OD2 ASP F 50 " model vdw 1.689 1.850 nonbonded pdb="HE21 GLN D 46 " pdb=" OD2 ASP D 50 " model vdw 1.689 1.850 nonbonded pdb="HE21 GLN B 46 " pdb=" OD2 ASP B 50 " model vdw 1.689 1.850 nonbonded pdb="HE21 GLN A 46 " pdb=" OD2 ASP A 50 " model vdw 1.689 1.850 ... (remaining 434890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 11.760 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 96.010 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16206 Z= 0.291 Angle : 0.724 6.250 21942 Z= 0.414 Chirality : 0.038 0.138 2406 Planarity : 0.004 0.051 2652 Dihedral : 14.218 80.564 5844 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.69 % Allowed : 2.06 % Favored : 97.25 % 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: -3.33 (0.18), residues: 1842 helix: -2.33 (0.12), residues: 1188 sheet: -2.52 (0.36), residues: 96 loop : -1.28 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 143 HIS 0.007 0.002 HIS D 104 PHE 0.014 0.002 PHE B 142 TYR 0.018 0.002 TYR F 106 ARG 0.009 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 327 time to evaluate : 2.726 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 HIS cc_start: 0.8667 (t70) cc_final: 0.8412 (t-90) REVERT: A 265 MET cc_start: 0.8901 (tpt) cc_final: 0.8576 (tpt) REVERT: A 404 GLN cc_start: 0.8789 (mt0) cc_final: 0.8310 (tm-30) REVERT: B 404 GLN cc_start: 0.8764 (mt0) cc_final: 0.8154 (tm-30) REVERT: C 37 MET cc_start: 0.8853 (mtp) cc_final: 0.8559 (tmm) REVERT: C 164 PHE cc_start: 0.8575 (t80) cc_final: 0.8370 (t80) REVERT: C 236 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: D 165 ASP cc_start: 0.9267 (OUTLIER) cc_final: 0.8826 (p0) REVERT: D 236 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: E 236 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: E 253 HIS cc_start: 0.8686 (t70) cc_final: 0.8418 (t-90) REVERT: F 253 HIS cc_start: 0.8611 (t70) cc_final: 0.8397 (t-90) REVERT: F 265 MET cc_start: 0.8883 (tpt) cc_final: 0.8406 (tpt) REVERT: F 404 GLN cc_start: 0.8758 (mt0) cc_final: 0.8220 (tm-30) outliers start: 12 outliers final: 7 residues processed: 333 average time/residue: 0.6755 time to fit residues: 323.7785 Evaluate side-chains 213 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16206 Z= 0.222 Angle : 0.572 5.001 21942 Z= 0.330 Chirality : 0.036 0.121 2406 Planarity : 0.004 0.032 2652 Dihedral : 4.814 20.565 2082 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1842 helix: -0.08 (0.14), residues: 1230 sheet: -2.11 (0.40), residues: 96 loop : -0.96 (0.31), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 168 HIS 0.012 0.002 HIS C 132 PHE 0.018 0.002 PHE A 156 TYR 0.017 0.002 TYR A 17 ARG 0.002 0.000 ARG F 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.506 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: 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: 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: 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: 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 165 ASP cc_start: 0.8943 (m-30) cc_final: 0.8542 (p0) REVERT: A 239 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8720 (mp10) REVERT: A 253 HIS cc_start: 0.8778 (t70) cc_final: 0.8472 (t70) REVERT: A 265 MET cc_start: 0.8711 (tpt) cc_final: 0.8367 (tpp) REVERT: A 343 MET cc_start: 0.8899 (ttm) cc_final: 0.8168 (ttm) REVERT: A 404 GLN cc_start: 0.8723 (mt0) cc_final: 0.8102 (tm-30) REVERT: B 241 LYS cc_start: 0.9307 (ptmt) cc_final: 0.8955 (ttmt) REVERT: B 265 MET cc_start: 0.8607 (tpt) cc_final: 0.8026 (tpt) REVERT: B 404 GLN cc_start: 0.8743 (mt0) cc_final: 0.8059 (tm-30) REVERT: C 241 LYS cc_start: 0.9239 (ptmt) cc_final: 0.8889 (ttmt) REVERT: D 396 GLU cc_start: 0.8861 (pm20) cc_final: 0.8394 (pm20) REVERT: E 253 HIS cc_start: 0.8655 (t70) cc_final: 0.8430 (t70) REVERT: F 165 ASP cc_start: 0.8653 (m-30) cc_final: 0.8398 (p0) REVERT: F 404 GLN cc_start: 0.8754 (mt0) cc_final: 0.8097 (tm-30) REVERT: F 408 ASN cc_start: 0.7272 (t0) cc_final: 0.7048 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.5529 time to fit residues: 229.0628 Evaluate side-chains 182 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16206 Z= 0.369 Angle : 0.652 5.546 21942 Z= 0.381 Chirality : 0.038 0.129 2406 Planarity : 0.004 0.042 2652 Dihedral : 5.019 19.496 2082 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.34 % Allowed : 2.75 % Favored : 96.91 % 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 (0.19), residues: 1842 helix: 0.30 (0.14), residues: 1284 sheet: -2.07 (0.38), residues: 96 loop : -1.61 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 168 HIS 0.012 0.002 HIS C 132 PHE 0.019 0.002 PHE E 156 TYR 0.015 0.002 TYR D 351 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 2.554 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7569 (t0) REVERT: A 165 ASP cc_start: 0.8986 (m-30) cc_final: 0.8517 (p0) REVERT: A 265 MET cc_start: 0.8672 (tpt) cc_final: 0.8449 (tpp) REVERT: A 404 GLN cc_start: 0.8725 (mt0) cc_final: 0.8086 (tm-30) REVERT: B 100 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 265 MET cc_start: 0.8506 (tpt) cc_final: 0.8217 (tpt) REVERT: B 343 MET cc_start: 0.8640 (ttm) cc_final: 0.8165 (ttm) REVERT: D 100 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7658 (t0) REVERT: E 100 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7745 (t0) REVERT: E 265 MET cc_start: 0.8786 (tpt) cc_final: 0.8435 (tpt) REVERT: E 375 MET cc_start: 0.8891 (ptm) cc_final: 0.8599 (ptp) REVERT: F 100 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7629 (t0) REVERT: F 404 GLN cc_start: 0.8744 (mt0) cc_final: 0.7999 (tm-30) outliers start: 6 outliers final: 1 residues processed: 232 average time/residue: 0.6182 time to fit residues: 215.7285 Evaluate side-chains 182 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16206 Z= 0.144 Angle : 0.474 4.764 21942 Z= 0.268 Chirality : 0.035 0.137 2406 Planarity : 0.003 0.028 2652 Dihedral : 4.376 15.536 2082 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.43 (0.19), residues: 1842 helix: 1.04 (0.14), residues: 1284 sheet: -1.89 (0.38), residues: 96 loop : -1.21 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.004 0.001 HIS C 132 PHE 0.013 0.001 PHE B 244 TYR 0.018 0.001 TYR C 264 ARG 0.002 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.681 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9041 (m-30) cc_final: 0.8498 (p0) REVERT: A 404 GLN cc_start: 0.8739 (mt0) cc_final: 0.8151 (tm-30) REVERT: B 343 MET cc_start: 0.8698 (ttm) cc_final: 0.7996 (ttm) REVERT: B 404 GLN cc_start: 0.8666 (mt0) cc_final: 0.7965 (tm-30) REVERT: C 404 GLN cc_start: 0.8798 (mt0) cc_final: 0.8117 (tm-30) REVERT: D 324 PHE cc_start: 0.8523 (t80) cc_final: 0.8226 (t80) REVERT: E 343 MET cc_start: 0.9078 (ttm) cc_final: 0.8739 (ttm) REVERT: E 375 MET cc_start: 0.8729 (ptm) cc_final: 0.8465 (ptp) REVERT: F 165 ASP cc_start: 0.8764 (m-30) cc_final: 0.8308 (p0) REVERT: F 404 GLN cc_start: 0.8762 (mt0) cc_final: 0.8041 (tm-30) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.6113 time to fit residues: 226.2566 Evaluate side-chains 197 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 161 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16206 Z= 0.305 Angle : 0.575 5.369 21942 Z= 0.329 Chirality : 0.036 0.148 2406 Planarity : 0.004 0.029 2652 Dihedral : 4.622 18.135 2082 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: 0.32 (0.19), residues: 1842 helix: 0.99 (0.14), residues: 1290 sheet: -1.59 (0.36), residues: 102 loop : -1.47 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 168 HIS 0.008 0.001 HIS C 132 PHE 0.016 0.002 PHE D 156 TYR 0.017 0.002 TYR C 351 ARG 0.003 0.000 ARG F 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.899 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8518 (tpp) cc_final: 0.8301 (tpt) REVERT: A 364 ASP cc_start: 0.7813 (m-30) cc_final: 0.7228 (m-30) REVERT: A 396 GLU cc_start: 0.9359 (pt0) cc_final: 0.9074 (pm20) REVERT: A 404 GLN cc_start: 0.8789 (mt0) cc_final: 0.8122 (tm-30) REVERT: B 236 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8548 (mp0) REVERT: B 241 LYS cc_start: 0.9173 (ptmt) cc_final: 0.8963 (tptp) REVERT: B 343 MET cc_start: 0.9007 (ttm) cc_final: 0.8298 (ttm) REVERT: B 404 GLN cc_start: 0.8726 (mt0) cc_final: 0.8007 (tm-30) REVERT: C 239 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8230 (mm-40) REVERT: C 337 MET cc_start: 0.8871 (tmm) cc_final: 0.8656 (tmm) REVERT: E 375 MET cc_start: 0.8814 (ptm) cc_final: 0.8604 (ptp) REVERT: F 343 MET cc_start: 0.9222 (ttm) cc_final: 0.8661 (ttm) REVERT: F 404 GLN cc_start: 0.8751 (mt0) cc_final: 0.7927 (tm-30) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.6146 time to fit residues: 205.5935 Evaluate side-chains 173 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16206 Z= 0.171 Angle : 0.488 4.302 21942 Z= 0.279 Chirality : 0.035 0.147 2406 Planarity : 0.003 0.027 2652 Dihedral : 4.401 15.936 2082 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1842 helix: 1.31 (0.14), residues: 1290 sheet: -1.37 (0.38), residues: 96 loop : -1.37 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 168 HIS 0.005 0.001 HIS C 132 PHE 0.011 0.001 PHE A 244 TYR 0.014 0.001 TYR C 351 ARG 0.003 0.000 ARG F 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.513 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9032 (m-30) cc_final: 0.8492 (p0) REVERT: A 265 MET cc_start: 0.8452 (tpp) cc_final: 0.8221 (tpt) REVERT: A 404 GLN cc_start: 0.8793 (mt0) cc_final: 0.8118 (tm-30) REVERT: B 236 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8606 (mp0) REVERT: B 265 MET cc_start: 0.8367 (tpp) cc_final: 0.8163 (tpt) REVERT: B 343 MET cc_start: 0.9029 (ttm) cc_final: 0.8335 (ttm) REVERT: B 404 GLN cc_start: 0.8711 (mt0) cc_final: 0.8039 (tm-30) REVERT: C 337 MET cc_start: 0.8902 (tmm) cc_final: 0.8678 (tmm) REVERT: D 265 MET cc_start: 0.8439 (tpp) cc_final: 0.7973 (tpt) REVERT: F 404 GLN cc_start: 0.8762 (mt0) cc_final: 0.7919 (tm-30) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.5949 time to fit residues: 203.2419 Evaluate side-chains 185 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16206 Z= 0.129 Angle : 0.450 4.117 21942 Z= 0.255 Chirality : 0.034 0.142 2406 Planarity : 0.003 0.029 2652 Dihedral : 4.154 14.061 2082 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 1.12 (0.20), residues: 1842 helix: 1.54 (0.14), residues: 1290 sheet: -1.02 (0.39), residues: 96 loop : -1.11 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 168 HIS 0.003 0.001 HIS D 132 PHE 0.016 0.001 PHE E 324 TYR 0.013 0.001 TYR E 332 ARG 0.002 0.000 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.810 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9016 (m-30) cc_final: 0.8449 (p0) REVERT: A 343 MET cc_start: 0.8958 (ttm) cc_final: 0.8184 (ttm) REVERT: B 265 MET cc_start: 0.8317 (tpp) cc_final: 0.8044 (tpt) REVERT: B 343 MET cc_start: 0.9071 (ttm) cc_final: 0.8253 (ttm) REVERT: B 404 GLN cc_start: 0.8701 (mt0) cc_final: 0.8039 (tm-30) REVERT: D 324 PHE cc_start: 0.8588 (t80) cc_final: 0.8262 (t80) REVERT: D 343 MET cc_start: 0.9004 (ttm) cc_final: 0.8326 (ttm) REVERT: F 165 ASP cc_start: 0.8887 (m-30) cc_final: 0.8312 (p0) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.5780 time to fit residues: 216.3109 Evaluate side-chains 186 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16206 Z= 0.200 Angle : 0.485 5.831 21942 Z= 0.278 Chirality : 0.034 0.131 2406 Planarity : 0.003 0.031 2652 Dihedral : 4.213 14.489 2082 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 1.21 (0.20), residues: 1842 helix: 1.58 (0.14), residues: 1296 sheet: -0.54 (0.41), residues: 96 loop : -1.13 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 168 HIS 0.016 0.001 HIS C 132 PHE 0.014 0.001 PHE E 324 TYR 0.014 0.001 TYR C 351 ARG 0.004 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.621 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: 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: 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: 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: 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 165 ASP cc_start: 0.9032 (m-30) cc_final: 0.8395 (p0) REVERT: B 236 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8593 (mp0) REVERT: B 265 MET cc_start: 0.8344 (tpp) cc_final: 0.8101 (tpt) REVERT: B 343 MET cc_start: 0.9069 (ttm) cc_final: 0.8187 (ttm) REVERT: B 404 GLN cc_start: 0.8725 (mt0) cc_final: 0.8067 (tm-30) REVERT: D 337 MET cc_start: 0.8868 (tmm) cc_final: 0.8590 (tmm) REVERT: D 343 MET cc_start: 0.9045 (ttm) cc_final: 0.8424 (ttm) REVERT: E 241 LYS cc_start: 0.9089 (ptmt) cc_final: 0.8726 (ttpt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5975 time to fit residues: 200.5292 Evaluate side-chains 174 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16206 Z= 0.133 Angle : 0.448 5.305 21942 Z= 0.254 Chirality : 0.034 0.143 2406 Planarity : 0.003 0.035 2652 Dihedral : 4.072 13.889 2082 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1842 helix: 1.71 (0.15), residues: 1290 sheet: -0.30 (0.41), residues: 96 loop : -1.04 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.015 0.001 HIS E 132 PHE 0.013 0.001 PHE E 324 TYR 0.020 0.001 TYR F 281 ARG 0.007 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.471 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8919 (m-30) cc_final: 0.8338 (p0) REVERT: B 236 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8561 (mp0) REVERT: B 265 MET cc_start: 0.8275 (tpp) cc_final: 0.8070 (tpt) REVERT: B 343 MET cc_start: 0.9107 (ttm) cc_final: 0.8329 (ttm) REVERT: B 375 MET cc_start: 0.8241 (ptm) cc_final: 0.7965 (ptp) REVERT: B 404 GLN cc_start: 0.8727 (mt0) cc_final: 0.8059 (tm-30) REVERT: C 343 MET cc_start: 0.8732 (ttm) cc_final: 0.8491 (ttm) REVERT: D 324 PHE cc_start: 0.8629 (t80) cc_final: 0.8302 (t80) REVERT: D 343 MET cc_start: 0.9047 (ttm) cc_final: 0.8452 (ttm) REVERT: E 241 LYS cc_start: 0.9075 (ptmt) cc_final: 0.8722 (ttpt) REVERT: F 165 ASP cc_start: 0.8889 (m-30) cc_final: 0.8234 (p0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.6370 time to fit residues: 222.0397 Evaluate side-chains 185 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16206 Z= 0.202 Angle : 0.494 6.085 21942 Z= 0.282 Chirality : 0.034 0.132 2406 Planarity : 0.003 0.031 2652 Dihedral : 4.159 14.558 2082 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.31 (0.20), residues: 1842 helix: 1.65 (0.14), residues: 1290 sheet: -0.30 (0.39), residues: 102 loop : -1.11 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 168 HIS 0.017 0.001 HIS E 132 PHE 0.017 0.001 PHE B 164 TYR 0.014 0.001 TYR C 332 ARG 0.007 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.729 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8883 (m-30) cc_final: 0.8294 (p0) REVERT: B 265 MET cc_start: 0.8301 (tpp) cc_final: 0.8027 (tpt) REVERT: B 343 MET cc_start: 0.9108 (ttm) cc_final: 0.8275 (ttm) REVERT: B 404 GLN cc_start: 0.8776 (mt0) cc_final: 0.8102 (tm-30) REVERT: C 236 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8429 (mp0) REVERT: D 337 MET cc_start: 0.8849 (tmm) cc_final: 0.8547 (tmm) REVERT: D 343 MET cc_start: 0.9092 (ttm) cc_final: 0.8803 (ttm) REVERT: E 241 LYS cc_start: 0.9071 (ptmt) cc_final: 0.8701 (ttpt) REVERT: F 37 MET cc_start: 0.8341 (tmm) cc_final: 0.8127 (tmm) REVERT: F 165 ASP cc_start: 0.8851 (m-30) cc_final: 0.8169 (p0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.6060 time to fit residues: 198.2759 Evaluate side-chains 172 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.065173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055400 restraints weight = 259174.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.057624 restraints weight = 109714.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058871 restraints weight = 61412.977| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16206 Z= 0.210 Angle : 0.501 5.912 21942 Z= 0.287 Chirality : 0.035 0.137 2406 Planarity : 0.003 0.034 2652 Dihedral : 4.197 14.676 2082 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 1.23 (0.20), residues: 1842 helix: 1.58 (0.14), residues: 1296 sheet: -0.19 (0.41), residues: 102 loop : -1.19 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.017 0.001 HIS E 132 PHE 0.021 0.001 PHE D 275 TYR 0.014 0.001 TYR D 332 ARG 0.006 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.20 seconds wall clock time: 108 minutes 31.15 seconds (6511.15 seconds total)