Starting phenix.real_space_refine on Wed Apr 10 10:38:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8i_29856/04_2024/8g8i_29856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8i_29856/04_2024/8g8i_29856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8i_29856/04_2024/8g8i_29856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8i_29856/04_2024/8g8i_29856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8i_29856/04_2024/8g8i_29856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8i_29856/04_2024/8g8i_29856.pdb" } resolution = 3.92 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= 0.031 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 12820 2.51 5 N 2970 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 464": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E ASP 293": "OD1" <-> "OD2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 339": "OD1" <-> "OD2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E GLU 422": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E GLU 449": "OE1" <-> "OE2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "E GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19335 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "B" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "D" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "E" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Time building chain proxies: 9.83, per 1000 atoms: 0.51 Number of scatterers: 19335 At special positions: 0 Unit cell: (83.19, 84.075, 238.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 3515 8.00 N 2970 7.00 C 12820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.79 Conformation dependent library (CDL) restraints added in 3.7 seconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 96.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.960A pdb=" N VAL A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 62 through 75 removed outlier: 4.042A pdb=" N ILE A 75 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.599A pdb=" N VAL A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.729A pdb=" N ASN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.572A pdb=" N ILE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.659A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 160 removed outlier: 3.568A pdb=" N LEU A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 175 through 194 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.189A pdb=" N GLU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.808A pdb=" N GLY A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.547A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 271 removed outlier: 4.295A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.757A pdb=" N ASN A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.950A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.650A pdb=" N GLY A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.636A pdb=" N LEU A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.628A pdb=" N VAL A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.617A pdb=" N ILE A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.653A pdb=" N ILE A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.506A pdb=" N GLU A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.843A pdb=" N VAL B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.645A pdb=" N ASN B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 75 Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.557A pdb=" N VAL B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 111 removed outlier: 3.516A pdb=" N ASN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.585A pdb=" N ILE B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 145 removed outlier: 3.573A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 160 Processing helix chain 'B' and resid 160 through 173 Processing helix chain 'B' and resid 175 through 194 Processing helix chain 'B' and resid 196 through 209 removed outlier: 3.937A pdb=" N ASN B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.686A pdb=" N GLY B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 Processing helix chain 'B' and resid 258 through 271 removed outlier: 4.136A pdb=" N ILE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 292 removed outlier: 3.530A pdb=" N VAL B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.882A pdb=" N ASN B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.901A pdb=" N ILE B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.725A pdb=" N VAL B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.508A pdb=" N SER B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.568A pdb=" N GLY B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.550A pdb=" N ILE B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 Processing helix chain 'B' and resid 420 through 439 Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.503A pdb=" N ASP B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.537A pdb=" N VAL C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 62 removed outlier: 3.545A pdb=" N ASN C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 75 removed outlier: 3.754A pdb=" N ILE C 75 " --> pdb=" O LYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 96 removed outlier: 3.595A pdb=" N VAL C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.528A pdb=" N ILE C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 145 removed outlier: 3.636A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 160 removed outlier: 3.544A pdb=" N LEU C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 173 Processing helix chain 'C' and resid 175 through 194 removed outlier: 4.019A pdb=" N GLU C 192 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 224 through 243 removed outlier: 3.922A pdb=" N GLY C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.510A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 271 removed outlier: 3.858A pdb=" N ILE C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 291 Processing helix chain 'C' and resid 294 through 307 removed outlier: 3.594A pdb=" N ASN C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.776A pdb=" N ILE C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 removed outlier: 3.783A pdb=" N VAL C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 356 removed outlier: 3.713A pdb=" N LEU C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.545A pdb=" N ILE C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 390 removed outlier: 3.644A pdb=" N VAL C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 388 " --> pdb=" O TRP C 384 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 405 removed outlier: 3.627A pdb=" N ILE C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 418 Processing helix chain 'C' and resid 420 through 439 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.550A pdb=" N VAL C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.813A pdb=" N ASN D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.526A pdb=" N VAL D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 62 through 75 removed outlier: 3.717A pdb=" N ILE D 75 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 95 Processing helix chain 'D' and resid 98 through 111 removed outlier: 3.522A pdb=" N ASN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 124 removed outlier: 3.707A pdb=" N ILE D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 145 removed outlier: 4.065A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 160 removed outlier: 3.575A pdb=" N LEU D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 Processing helix chain 'D' and resid 175 through 194 removed outlier: 3.899A pdb=" N GLU D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 209 through 222 removed outlier: 3.969A pdb=" N GLU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.500A pdb=" N VAL D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 removed outlier: 3.570A pdb=" N LEU D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.679A pdb=" N ILE D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 292 removed outlier: 3.600A pdb=" N VAL D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 306 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.533A pdb=" N ILE D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 340 Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 371 through 390 removed outlier: 3.687A pdb=" N LYS D 383 " --> pdb=" O PHE D 379 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 388 " --> pdb=" O TRP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 404 removed outlier: 3.638A pdb=" N SER D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 420 through 439 removed outlier: 3.506A pdb=" N GLY D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 454 removed outlier: 4.213A pdb=" N ASP D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 465 Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.810A pdb=" N ASN E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 26 Processing helix chain 'E' and resid 28 through 47 removed outlier: 3.693A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 62 removed outlier: 3.633A pdb=" N ASN E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 4.073A pdb=" N ILE E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 94 removed outlier: 3.505A pdb=" N VAL E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 109 Processing helix chain 'E' and resid 111 through 124 removed outlier: 4.099A pdb=" N ILE E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 145 removed outlier: 3.827A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 160 removed outlier: 3.584A pdb=" N ASN E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 175 through 194 removed outlier: 3.554A pdb=" N GLU E 192 " --> pdb=" O TYR E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.612A pdb=" N SER E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 222 removed outlier: 3.509A pdb=" N GLU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 243 Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.600A pdb=" N ILE E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 292 removed outlier: 3.668A pdb=" N VAL E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 305 Processing helix chain 'E' and resid 307 through 320 Processing helix chain 'E' and resid 322 through 341 removed outlier: 3.677A pdb=" N GLY E 341 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.712A pdb=" N ASN E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 369 Processing helix chain 'E' and resid 371 through 389 Processing helix chain 'E' and resid 392 through 404 Processing helix chain 'E' and resid 405 through 419 removed outlier: 3.532A pdb=" N GLY E 419 " --> pdb=" O TRP E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 438 Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 454 through 465 1554 hydrogen bonds defined for protein. 4662 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: 6.49 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6075 1.34 - 1.46: 3804 1.46 - 1.58: 9771 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 19710 Sorted by residual: bond pdb=" CA ASN C 223 " pdb=" C ASN C 223 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.06e+00 bond pdb=" C GLY C 438 " pdb=" N GLY C 439 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.53e-01 bond pdb=" CA ASN B 196 " pdb=" CB ASN B 196 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.35e-02 5.49e+03 7.41e-01 bond pdb=" CG1 ILE A 53 " pdb=" CD1 ILE A 53 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.34e-01 bond pdb=" N ASN B 294 " pdb=" CA ASN B 294 " ideal model delta sigma weight residual 1.463 1.455 0.007 8.80e-03 1.29e+04 7.01e-01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.18: 348 107.18 - 113.92: 11680 113.92 - 120.67: 8847 120.67 - 127.42: 5563 127.42 - 134.16: 182 Bond angle restraints: 26620 Sorted by residual: angle pdb=" N ARG E 371 " pdb=" CA ARG E 371 " pdb=" C ARG E 371 " ideal model delta sigma weight residual 112.97 109.88 3.09 1.06e+00 8.90e-01 8.52e+00 angle pdb=" N ILE E 271 " pdb=" CA ILE E 271 " pdb=" C ILE E 271 " ideal model delta sigma weight residual 112.98 109.38 3.60 1.25e+00 6.40e-01 8.27e+00 angle pdb=" N LYS B 175 " pdb=" CA LYS B 175 " pdb=" C LYS B 175 " ideal model delta sigma weight residual 112.97 110.23 2.74 1.06e+00 8.90e-01 6.67e+00 angle pdb=" N ILE B 26 " pdb=" CA ILE B 26 " pdb=" C ILE B 26 " ideal model delta sigma weight residual 112.98 109.93 3.05 1.25e+00 6.40e-01 5.97e+00 angle pdb=" N ARG D 126 " pdb=" CA ARG D 126 " pdb=" C ARG D 126 " ideal model delta sigma weight residual 110.44 107.71 2.73 1.20e+00 6.94e-01 5.17e+00 ... (remaining 26615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10599 17.97 - 35.94: 1013 35.94 - 53.91: 162 53.91 - 71.89: 84 71.89 - 89.86: 52 Dihedral angle restraints: 11910 sinusoidal: 5120 harmonic: 6790 Sorted by residual: dihedral pdb=" CA ASN A 147 " pdb=" C ASN A 147 " pdb=" N PRO A 148 " pdb=" CA PRO A 148 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU C 452 " pdb=" C LEU C 452 " pdb=" N LEU C 453 " pdb=" CA LEU C 453 " ideal model delta harmonic sigma weight residual 180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA GLU A 270 " pdb=" C GLU A 270 " pdb=" N ILE A 271 " pdb=" CA ILE A 271 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 11907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1568 0.027 - 0.053: 981 0.053 - 0.080: 397 0.080 - 0.106: 80 0.106 - 0.133: 34 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" C PRO A 148 " pdb=" CB PRO A 148 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CB ILE A 75 " pdb=" CA ILE A 75 " pdb=" CG1 ILE A 75 " pdb=" CG2 ILE A 75 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CG LEU D 349 " pdb=" CB LEU D 349 " pdb=" CD1 LEU D 349 " pdb=" CD2 LEU D 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 3057 not shown) Planarity restraints: 3315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 258 " 0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO C 259 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 160 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO A 161 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 454 " 0.033 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 455 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " 0.029 5.00e-02 4.00e+02 ... (remaining 3312 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3786 2.78 - 3.31: 19764 3.31 - 3.84: 31482 3.84 - 4.37: 33985 4.37 - 4.90: 59548 Nonbonded interactions: 148565 Sorted by model distance: nonbonded pdb=" O GLU A 351 " pdb=" OG SER A 355 " model vdw 2.245 2.440 nonbonded pdb=" O LYS A 302 " pdb=" OG SER A 306 " model vdw 2.261 2.440 nonbonded pdb=" O LYS D 204 " pdb=" OG SER D 208 " model vdw 2.264 2.440 nonbonded pdb=" O SER A 61 " pdb=" OG SER A 61 " model vdw 2.278 2.440 nonbonded pdb=" O SER E 110 " pdb=" OG SER E 110 " model vdw 2.308 2.440 ... (remaining 148560 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.260 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 51.370 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.004 0.033 19710 Z= 0.221 Angle : 0.551 7.405 26620 Z= 0.308 Chirality : 0.039 0.133 3060 Planarity : 0.004 0.057 3315 Dihedral : 16.256 89.857 7470 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 2315 helix: 0.22 (0.10), residues: 2105 sheet: None (None), residues: 0 loop : -3.55 (0.34), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 415 HIS 0.004 0.001 HIS A 397 PHE 0.014 0.002 PHE A 379 TYR 0.010 0.001 TYR B 237 ARG 0.003 0.000 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 125 ASN cc_start: 0.7336 (m-40) cc_final: 0.7110 (m-40) REVERT: A 156 LEU cc_start: 0.8386 (tp) cc_final: 0.8137 (tp) REVERT: B 3 TYR cc_start: 0.6960 (t80) cc_final: 0.6655 (t80) REVERT: B 162 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 16 ILE cc_start: 0.8639 (mm) cc_final: 0.8365 (mm) REVERT: C 187 LEU cc_start: 0.8290 (tp) cc_final: 0.7931 (tt) REVERT: D 257 SER cc_start: 0.7783 (p) cc_final: 0.7335 (t) REVERT: E 89 LYS cc_start: 0.7495 (tmtt) cc_final: 0.7267 (tmtt) REVERT: E 217 LEU cc_start: 0.8387 (mt) cc_final: 0.8087 (mt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.3293 time to fit residues: 187.4941 Evaluate side-chains 190 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 147 ASN B 125 ASN B 272 ASN C 49 ASN C 209 ASN D 13 ASN D 146 ASN D 209 ASN D 391 ASN E 49 ASN E 321 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19710 Z= 0.257 Angle : 0.575 9.919 26620 Z= 0.285 Chirality : 0.039 0.177 3060 Planarity : 0.003 0.040 3315 Dihedral : 3.986 22.262 2400 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.52 % Allowed : 9.66 % Favored : 88.83 % 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: 1.77 (0.17), residues: 2315 helix: 1.49 (0.10), residues: 2170 sheet: None (None), residues: 0 loop : -3.36 (0.41), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 219 HIS 0.002 0.001 HIS A 368 PHE 0.014 0.001 PHE D 458 TYR 0.018 0.002 TYR C 188 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 226 time to evaluate : 2.275 Fit side-chains REVERT: A 123 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 125 ASN cc_start: 0.7474 (m-40) cc_final: 0.7236 (m-40) REVERT: B 3 TYR cc_start: 0.6871 (t80) cc_final: 0.6646 (t80) REVERT: B 69 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6935 (mp) REVERT: B 162 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7016 (mm-30) REVERT: C 16 ILE cc_start: 0.8900 (mm) cc_final: 0.8453 (mm) REVERT: C 208 SER cc_start: 0.8505 (p) cc_final: 0.8081 (m) REVERT: C 355 SER cc_start: 0.8677 (p) cc_final: 0.8424 (m) REVERT: C 452 LEU cc_start: 0.8541 (tp) cc_final: 0.8221 (tt) REVERT: D 12 GLU cc_start: 0.7216 (tp30) cc_final: 0.6960 (tp30) REVERT: D 114 ILE cc_start: 0.9075 (mm) cc_final: 0.8862 (mt) REVERT: D 125 ASN cc_start: 0.7796 (m-40) cc_final: 0.6358 (t0) REVERT: D 146 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7110 (p0) REVERT: D 257 SER cc_start: 0.7831 (p) cc_final: 0.7533 (t) REVERT: E 89 LYS cc_start: 0.7721 (tmtt) cc_final: 0.7440 (tmtt) REVERT: E 200 LEU cc_start: 0.8468 (tt) cc_final: 0.7983 (mm) REVERT: E 290 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8034 (tt0) outliers start: 33 outliers final: 19 residues processed: 251 average time/residue: 0.3011 time to fit residues: 119.0006 Evaluate side-chains 186 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 463 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN D 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19710 Z= 0.177 Angle : 0.478 8.644 26620 Z= 0.235 Chirality : 0.037 0.131 3060 Planarity : 0.003 0.036 3315 Dihedral : 3.654 19.652 2400 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.33 % Allowed : 12.46 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.17), residues: 2315 helix: 2.12 (0.10), residues: 2175 sheet: None (None), residues: 0 loop : -3.43 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 384 HIS 0.002 0.001 HIS B 368 PHE 0.016 0.001 PHE E 458 TYR 0.012 0.001 TYR A 249 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 2.139 Fit side-chains REVERT: A 123 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 125 ASN cc_start: 0.7400 (m-40) cc_final: 0.7156 (m110) REVERT: B 69 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6908 (mp) REVERT: C 16 ILE cc_start: 0.8940 (mm) cc_final: 0.8398 (mm) REVERT: C 187 LEU cc_start: 0.8534 (tp) cc_final: 0.8288 (tt) REVERT: C 208 SER cc_start: 0.8483 (p) cc_final: 0.8118 (m) REVERT: C 251 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8051 (mt) REVERT: C 355 SER cc_start: 0.8717 (p) cc_final: 0.8486 (m) REVERT: D 12 GLU cc_start: 0.7263 (tp30) cc_final: 0.7010 (tp30) REVERT: D 37 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6286 (tt0) REVERT: D 114 ILE cc_start: 0.9054 (mm) cc_final: 0.8850 (mt) REVERT: D 125 ASN cc_start: 0.7925 (m-40) cc_final: 0.6372 (t0) REVERT: D 143 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7431 (ttm170) REVERT: D 146 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7058 (p0) REVERT: D 257 SER cc_start: 0.7796 (p) cc_final: 0.7520 (t) REVERT: E 89 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7404 (tmtt) REVERT: E 200 LEU cc_start: 0.8525 (tt) cc_final: 0.7642 (mm) REVERT: E 290 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8066 (tt0) outliers start: 29 outliers final: 19 residues processed: 219 average time/residue: 0.3085 time to fit residues: 106.6208 Evaluate side-chains 191 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 169 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 199 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN B 272 ASN D 146 ASN D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19710 Z= 0.226 Angle : 0.518 9.904 26620 Z= 0.251 Chirality : 0.038 0.167 3060 Planarity : 0.003 0.032 3315 Dihedral : 3.637 20.574 2400 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.16 % Allowed : 13.84 % Favored : 84.00 % 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: 3.00 (0.17), residues: 2315 helix: 2.31 (0.10), residues: 2170 sheet: None (None), residues: 0 loop : -3.60 (0.45), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 219 HIS 0.003 0.001 HIS A 368 PHE 0.011 0.001 PHE C 280 TYR 0.020 0.001 TYR E 3 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 2.105 Fit side-chains REVERT: A 123 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 125 ASN cc_start: 0.7343 (m-40) cc_final: 0.7101 (m110) REVERT: B 69 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6882 (mp) REVERT: C 16 ILE cc_start: 0.8989 (mm) cc_final: 0.8440 (mm) REVERT: C 208 SER cc_start: 0.8545 (p) cc_final: 0.8274 (m) REVERT: C 355 SER cc_start: 0.8736 (p) cc_final: 0.8504 (m) REVERT: D 125 ASN cc_start: 0.7917 (m-40) cc_final: 0.6440 (t0) REVERT: D 146 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7162 (p0) REVERT: D 352 LEU cc_start: 0.8438 (tp) cc_final: 0.8204 (tp) REVERT: E 89 LYS cc_start: 0.7738 (tmtt) cc_final: 0.7443 (tmtt) REVERT: E 123 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7148 (tm-30) REVERT: E 200 LEU cc_start: 0.8562 (tt) cc_final: 0.7968 (mm) outliers start: 47 outliers final: 32 residues processed: 200 average time/residue: 0.3210 time to fit residues: 102.8658 Evaluate side-chains 179 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 433 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19710 Z= 0.173 Angle : 0.467 10.785 26620 Z= 0.227 Chirality : 0.036 0.152 3060 Planarity : 0.002 0.031 3315 Dihedral : 3.470 18.840 2400 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.98 % Allowed : 14.80 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.17), residues: 2315 helix: 2.56 (0.10), residues: 2170 sheet: None (None), residues: 0 loop : -3.58 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 23 HIS 0.002 0.001 HIS B 368 PHE 0.009 0.001 PHE A 25 TYR 0.013 0.001 TYR E 3 ARG 0.005 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 176 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 125 ASN cc_start: 0.7324 (m-40) cc_final: 0.5907 (t0) REVERT: B 69 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6831 (mp) REVERT: C 16 ILE cc_start: 0.9006 (mm) cc_final: 0.8445 (mm) REVERT: C 208 SER cc_start: 0.8593 (p) cc_final: 0.8329 (m) REVERT: C 355 SER cc_start: 0.8712 (p) cc_final: 0.8503 (m) REVERT: D 37 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6394 (tt0) REVERT: D 146 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.7111 (p0) REVERT: D 352 LEU cc_start: 0.8360 (tp) cc_final: 0.8144 (tp) REVERT: E 89 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7411 (tmtt) REVERT: E 123 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7130 (tm-30) REVERT: E 200 LEU cc_start: 0.8515 (tt) cc_final: 0.7920 (mm) REVERT: E 244 ASP cc_start: 0.5469 (p0) cc_final: 0.5233 (p0) REVERT: E 344 MET cc_start: 0.5503 (tpp) cc_final: 0.5118 (tpp) outliers start: 43 outliers final: 30 residues processed: 207 average time/residue: 0.3066 time to fit residues: 100.0160 Evaluate side-chains 180 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19710 Z= 0.190 Angle : 0.475 10.758 26620 Z= 0.231 Chirality : 0.037 0.143 3060 Planarity : 0.002 0.029 3315 Dihedral : 3.439 18.676 2400 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.25 % Allowed : 15.68 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.17), residues: 2315 helix: 2.64 (0.10), residues: 2170 sheet: None (None), residues: 0 loop : -3.52 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 384 HIS 0.002 0.001 HIS B 368 PHE 0.017 0.001 PHE E 458 TYR 0.012 0.001 TYR E 3 ARG 0.003 0.000 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 2.337 Fit side-chains REVERT: A 123 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 125 ASN cc_start: 0.7250 (m-40) cc_final: 0.5896 (t0) REVERT: A 344 MET cc_start: 0.6597 (tpp) cc_final: 0.6300 (tpp) REVERT: B 69 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6858 (mp) REVERT: C 16 ILE cc_start: 0.9007 (mm) cc_final: 0.8429 (mm) REVERT: C 143 ARG cc_start: 0.7393 (tpt-90) cc_final: 0.7154 (ttm170) REVERT: C 208 SER cc_start: 0.8612 (p) cc_final: 0.8343 (m) REVERT: D 37 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6424 (tt0) REVERT: D 143 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7505 (ttm170) REVERT: D 146 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.7032 (p0) REVERT: D 352 LEU cc_start: 0.8374 (tp) cc_final: 0.8143 (tp) REVERT: E 89 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7417 (tmtt) REVERT: E 123 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7178 (tm-30) REVERT: E 143 ARG cc_start: 0.8075 (tpp80) cc_final: 0.7839 (tpt-90) REVERT: E 200 LEU cc_start: 0.8482 (tt) cc_final: 0.7861 (mm) REVERT: E 344 MET cc_start: 0.5626 (tpp) cc_final: 0.5188 (tpp) outliers start: 49 outliers final: 38 residues processed: 194 average time/residue: 0.2967 time to fit residues: 91.8045 Evaluate side-chains 189 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 chunk 162 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN E 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19710 Z= 0.124 Angle : 0.438 11.109 26620 Z= 0.211 Chirality : 0.035 0.138 3060 Planarity : 0.002 0.028 3315 Dihedral : 3.197 15.542 2400 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.75 % Allowed : 16.41 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.17), residues: 2315 helix: 2.91 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.84 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 384 HIS 0.001 0.000 HIS B 368 PHE 0.006 0.001 PHE A 311 TYR 0.015 0.001 TYR C 188 ARG 0.003 0.000 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 183 time to evaluate : 2.287 Fit side-chains REVERT: A 12 GLU cc_start: 0.6907 (tp30) cc_final: 0.6679 (tp30) REVERT: A 123 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 125 ASN cc_start: 0.7073 (m-40) cc_final: 0.5770 (t0) REVERT: B 69 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6730 (mp) REVERT: B 393 MET cc_start: 0.6946 (mmm) cc_final: 0.6702 (mmt) REVERT: C 16 ILE cc_start: 0.8978 (mm) cc_final: 0.8413 (mm) REVERT: C 102 LEU cc_start: 0.7908 (mp) cc_final: 0.7479 (tt) REVERT: D 29 GLU cc_start: 0.6237 (pm20) cc_final: 0.6008 (pm20) REVERT: D 37 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6582 (tt0) REVERT: D 352 LEU cc_start: 0.8203 (tp) cc_final: 0.7980 (tp) REVERT: E 89 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7477 (tmtt) REVERT: E 123 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7056 (tm-30) REVERT: E 143 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7820 (tpt-90) REVERT: E 200 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7888 (mm) REVERT: E 344 MET cc_start: 0.5595 (tpp) cc_final: 0.5154 (tpp) outliers start: 38 outliers final: 29 residues processed: 206 average time/residue: 0.2882 time to fit residues: 96.3107 Evaluate side-chains 190 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19710 Z= 0.150 Angle : 0.486 11.133 26620 Z= 0.230 Chirality : 0.036 0.143 3060 Planarity : 0.002 0.027 3315 Dihedral : 3.169 15.436 2400 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.98 % Allowed : 17.29 % Favored : 80.74 % 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: 4.01 (0.17), residues: 2315 helix: 2.96 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.77 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 384 HIS 0.002 0.001 HIS A 368 PHE 0.015 0.001 PHE B 85 TYR 0.010 0.001 TYR E 3 ARG 0.003 0.000 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 174 time to evaluate : 2.088 Fit side-chains REVERT: A 12 GLU cc_start: 0.6946 (tp30) cc_final: 0.6734 (tp30) REVERT: A 123 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 125 ASN cc_start: 0.7005 (m-40) cc_final: 0.5776 (t0) REVERT: B 69 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6827 (mp) REVERT: B 393 MET cc_start: 0.6993 (mmm) cc_final: 0.6707 (mmt) REVERT: C 16 ILE cc_start: 0.8996 (mm) cc_final: 0.8413 (mm) REVERT: C 102 LEU cc_start: 0.7928 (mp) cc_final: 0.7455 (tt) REVERT: C 208 SER cc_start: 0.8595 (p) cc_final: 0.8323 (m) REVERT: C 461 LEU cc_start: 0.8733 (tp) cc_final: 0.8272 (tp) REVERT: D 37 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6502 (tt0) REVERT: D 143 ARG cc_start: 0.7818 (tpt-90) cc_final: 0.7504 (ttm170) REVERT: E 89 LYS cc_start: 0.7771 (tmtt) cc_final: 0.7471 (tmtt) REVERT: E 123 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7073 (tm-30) REVERT: E 143 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7906 (tpt-90) REVERT: E 200 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7876 (mm) REVERT: E 344 MET cc_start: 0.5694 (tpp) cc_final: 0.5239 (tpp) outliers start: 43 outliers final: 34 residues processed: 203 average time/residue: 0.2890 time to fit residues: 94.7755 Evaluate side-chains 192 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 19710 Z= 0.149 Angle : 0.481 10.924 26620 Z= 0.226 Chirality : 0.036 0.144 3060 Planarity : 0.002 0.026 3315 Dihedral : 3.132 15.314 2400 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.93 % Allowed : 17.66 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.17), residues: 2315 helix: 3.00 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.76 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 219 HIS 0.002 0.001 HIS B 368 PHE 0.013 0.001 PHE D 213 TYR 0.010 0.001 TYR E 3 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 2.272 Fit side-chains REVERT: A 12 GLU cc_start: 0.6932 (tp30) cc_final: 0.6723 (tp30) REVERT: A 123 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 125 ASN cc_start: 0.7027 (m-40) cc_final: 0.5813 (t0) REVERT: B 69 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6822 (mp) REVERT: B 393 MET cc_start: 0.6930 (mmm) cc_final: 0.6668 (mmt) REVERT: C 16 ILE cc_start: 0.8985 (mm) cc_final: 0.8381 (mm) REVERT: C 208 SER cc_start: 0.8572 (p) cc_final: 0.8304 (m) REVERT: C 442 MET cc_start: 0.6918 (mmt) cc_final: 0.6655 (tpp) REVERT: C 461 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8530 (tp) REVERT: D 37 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6506 (tt0) REVERT: E 89 LYS cc_start: 0.7771 (tmtt) cc_final: 0.7457 (tmtt) REVERT: E 113 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7472 (mt-10) REVERT: E 123 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7061 (tm-30) REVERT: E 143 ARG cc_start: 0.8087 (tpp80) cc_final: 0.7877 (tpt-90) REVERT: E 200 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7863 (mm) REVERT: E 344 MET cc_start: 0.5659 (tpp) cc_final: 0.5255 (tpp) outliers start: 42 outliers final: 33 residues processed: 186 average time/residue: 0.2848 time to fit residues: 86.5015 Evaluate side-chains 188 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 229 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19710 Z= 0.201 Angle : 0.521 10.853 26620 Z= 0.245 Chirality : 0.037 0.154 3060 Planarity : 0.002 0.025 3315 Dihedral : 3.290 17.098 2400 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.89 % Allowed : 17.66 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.17), residues: 2315 helix: 2.90 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -2.66 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 219 HIS 0.003 0.001 HIS B 368 PHE 0.013 0.001 PHE B 85 TYR 0.010 0.001 TYR E 3 ARG 0.002 0.000 ARG E 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 2.306 Fit side-chains REVERT: A 12 GLU cc_start: 0.6995 (tp30) cc_final: 0.6791 (tp30) REVERT: A 123 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 125 ASN cc_start: 0.7289 (m-40) cc_final: 0.5980 (t0) REVERT: B 69 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6882 (mp) REVERT: B 393 MET cc_start: 0.7015 (mmm) cc_final: 0.6720 (mmt) REVERT: C 16 ILE cc_start: 0.9012 (mm) cc_final: 0.8420 (mm) REVERT: C 251 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7746 (tt) REVERT: C 324 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: C 442 MET cc_start: 0.7003 (mmt) cc_final: 0.6726 (tpp) REVERT: C 461 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8555 (tp) REVERT: D 217 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (mm) REVERT: E 89 LYS cc_start: 0.7787 (tmtt) cc_final: 0.7420 (tmtt) REVERT: E 123 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6726 (tm-30) REVERT: E 143 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7928 (tpt-90) REVERT: E 344 MET cc_start: 0.5760 (tpp) cc_final: 0.5290 (tpp) outliers start: 41 outliers final: 33 residues processed: 189 average time/residue: 0.3145 time to fit residues: 96.5426 Evaluate side-chains 188 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN C 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142181 restraints weight = 22998.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141367 restraints weight = 31156.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141614 restraints weight = 30341.635| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19710 Z= 0.239 Angle : 0.560 11.465 26620 Z= 0.264 Chirality : 0.038 0.180 3060 Planarity : 0.003 0.026 3315 Dihedral : 3.434 19.442 2400 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.07 % Allowed : 17.70 % Favored : 80.23 % 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: 3.71 (0.17), residues: 2315 helix: 2.75 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -2.81 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 384 HIS 0.003 0.001 HIS B 368 PHE 0.014 0.001 PHE B 85 TYR 0.009 0.001 TYR E 3 ARG 0.003 0.000 ARG E 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.45 seconds wall clock time: 57 minutes 50.40 seconds (3470.40 seconds total)