Starting phenix.real_space_refine on Sun Mar 10 14:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/03_2024/6pos_20418_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/03_2024/6pos_20418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/03_2024/6pos_20418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/03_2024/6pos_20418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/03_2024/6pos_20418_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/03_2024/6pos_20418_trim_updated.pdb" } resolution = 4.12 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= 1.000 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 119 5.16 5 C 16766 2.51 5 N 4555 2.21 5 O 5193 1.98 5 H 26853 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 392": "OD1" <-> "OD2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C ASP 392": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 392": "OD1" <-> "OD2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 86": "OD1" <-> "OD2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N ASP 18": "OD1" <-> "OD2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53503 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5273 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 2 Chain: "B" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5409 Classifications: {'peptide': 351} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain breaks: 1 Chain: "C" Number of atoms: 5413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5413 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 1 Chain: "D" Number of atoms: 5401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5401 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 1 Chain: "E" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5409 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5244 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "S" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 59 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.14, per 1000 atoms: 0.32 Number of scatterers: 53503 At special positions: 0 Unit cell: (146.16, 140.36, 140.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 17 15.00 O 5193 8.00 N 4555 7.00 C 16766 6.00 H 26853 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.75 Conformation dependent library (CDL) restraints added in 4.5 seconds 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 37 sheets defined 43.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.705A pdb=" N ASP A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 removed outlier: 3.536A pdb=" N LEU A 99 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.931A pdb=" N GLU A 216 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.926A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.565A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.678A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.814A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.526A pdb=" N LEU A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.697A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.791A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.564A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.693A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.525A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 186 through 189 removed outlier: 3.578A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.699A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.656A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.580A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 298' Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.571A pdb=" N ILE B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 352 through 365 removed outlier: 3.734A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.686A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.727A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.524A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.541A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.568A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.868A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 removed outlier: 3.718A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.770A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 removed outlier: 3.648A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 342 Processing helix chain 'C' and resid 352 through 365 removed outlier: 4.006A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.638A pdb=" N ALA C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.543A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 404' Processing helix chain 'D' and resid 67 through 77 removed outlier: 3.706A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 100 removed outlier: 3.906A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.618A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.878A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 263 removed outlier: 3.563A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 289 removed outlier: 3.716A pdb=" N ALA D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.831A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 319 through 325 removed outlier: 3.691A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 352 through 365 removed outlier: 3.758A pdb=" N ALA D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 83 through 100 Processing helix chain 'E' and resid 125 through 136 removed outlier: 3.525A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.666A pdb=" N ILE E 161 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'E' and resid 205 through 216 removed outlier: 3.698A pdb=" N ALA E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.652A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 298 removed outlier: 3.706A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 319 through 325 removed outlier: 3.783A pdb=" N ILE E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 342 Processing helix chain 'E' and resid 352 through 365 removed outlier: 4.085A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.739A pdb=" N ALA E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 400 through 404 removed outlier: 3.587A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 404' Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.577A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 101 removed outlier: 3.626A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 136 removed outlier: 3.639A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.544A pdb=" N LEU F 165 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 189 Processing helix chain 'F' and resid 205 through 216 removed outlier: 3.525A pdb=" N GLN F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 212 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS F 213 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 216 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 254 through 261 removed outlier: 3.581A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 Processing helix chain 'F' and resid 292 through 298 removed outlier: 3.829A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 352 through 365 removed outlier: 3.523A pdb=" N ASP F 356 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 379 Processing helix chain 'F' and resid 381 through 387 Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.640A pdb=" N LEU H 23 " --> pdb=" O ILE H 19 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.622A pdb=" N ALA H 45 " --> pdb=" O ASN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.663A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 132 through 157 Processing helix chain 'H' and resid 161 through 167 Processing helix chain 'H' and resid 176 through 181 removed outlier: 3.620A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.545A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 removed outlier: 3.624A pdb=" N ALA I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.627A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 104 Processing helix chain 'I' and resid 132 through 157 Processing helix chain 'I' and resid 161 through 167 Processing helix chain 'I' and resid 176 through 181 removed outlier: 3.680A pdb=" N VAL I 180 " --> pdb=" O ALA I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.600A pdb=" N LEU J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 removed outlier: 3.622A pdb=" N ALA J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.645A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 104 Processing helix chain 'J' and resid 132 through 157 removed outlier: 3.525A pdb=" N ILE J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 167 Processing helix chain 'J' and resid 176 through 181 removed outlier: 3.655A pdb=" N VAL J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.588A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 removed outlier: 3.677A pdb=" N ALA K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.640A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 104 Processing helix chain 'K' and resid 132 through 157 Processing helix chain 'K' and resid 161 through 167 Processing helix chain 'K' and resid 176 through 181 removed outlier: 3.678A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.512A pdb=" N LEU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.638A pdb=" N ALA L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.698A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 104 Processing helix chain 'L' and resid 132 through 157 Processing helix chain 'L' and resid 161 through 167 Processing helix chain 'L' and resid 176 through 181 removed outlier: 3.702A pdb=" N VAL L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.550A pdb=" N LEU M 23 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.584A pdb=" N ALA M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.664A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 132 through 157 Processing helix chain 'M' and resid 161 through 167 Processing helix chain 'M' and resid 176 through 181 removed outlier: 3.657A pdb=" N VAL M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.599A pdb=" N LEU N 23 " --> pdb=" O ILE N 19 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 removed outlier: 3.526A pdb=" N ALA N 45 " --> pdb=" O ASN N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 82 removed outlier: 3.640A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 104 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 167 Processing helix chain 'N' and resid 176 through 181 removed outlier: 3.635A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 115 through 117 removed outlier: 3.613A pdb=" N ILE A 115 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 395 through 397 Processing sheet with id= C, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.094A pdb=" N VAL B 310 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE B 118 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA B 312 " --> pdb=" O ILE B 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 140 through 144 removed outlier: 7.115A pdb=" N ILE B 180 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA B 143 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR B 182 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU B 244 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 183 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 246 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.761A pdb=" N ILE B 398 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 412 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL B 396 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 410 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 115 through 117 Processing sheet with id= G, first strand: chain 'C' and resid 393 through 397 removed outlier: 7.095A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 115 through 117 Processing sheet with id= I, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.192A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.525A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.943A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 395 through 397 removed outlier: 3.533A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.571A pdb=" N VAL F 310 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE F 118 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 312 " --> pdb=" O ILE F 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 140 through 144 removed outlier: 7.260A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA F 143 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR F 182 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE F 246 " --> pdb=" O ILE F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.858A pdb=" N ALA F 220 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL F 238 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 395 through 397 removed outlier: 3.513A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.825A pdb=" N ARG H 15 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.700A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 119 through 121 Processing sheet with id= T, first strand: chain 'I' and resid 5 through 9 removed outlier: 3.808A pdb=" N ARG I 15 " --> pdb=" O GLU I 8 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.644A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= W, first strand: chain 'J' and resid 5 through 9 removed outlier: 3.817A pdb=" N ARG J 15 " --> pdb=" O GLU J 8 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.583A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= Z, first strand: chain 'K' and resid 5 through 9 removed outlier: 3.768A pdb=" N ARG K 15 " --> pdb=" O GLU K 8 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.588A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 119 through 121 Processing sheet with id= AC, first strand: chain 'L' and resid 5 through 9 removed outlier: 3.746A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.635A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 119 through 121 Processing sheet with id= AF, first strand: chain 'M' and resid 5 through 9 removed outlier: 3.841A pdb=" N ARG M 15 " --> pdb=" O GLU M 8 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.546A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AI, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.857A pdb=" N ARG N 15 " --> pdb=" O GLU N 8 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.617A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 119 through 121 890 hydrogen bonds defined for protein. 2400 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: 15.96 Time building geometry restraints manager: 34.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 26833 1.05 - 1.27: 4686 1.27 - 1.50: 10466 1.50 - 1.72: 11682 1.72 - 1.95: 213 Bond restraints: 53880 Sorted by residual: bond pdb=" N SER B 62 " pdb=" H1 SER B 62 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" N GLU D 234 " pdb=" CA GLU D 234 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.29e-02 6.01e+03 7.59e+00 bond pdb=" N LEU D 236 " pdb=" CA LEU D 236 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" C VAL C 238 " pdb=" N ASP C 239 " ideal model delta sigma weight residual 1.331 1.364 -0.034 1.29e-02 6.01e+03 6.81e+00 bond pdb=" N PHE D 235 " pdb=" CA PHE D 235 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.29e-02 6.01e+03 6.62e+00 ... (remaining 53875 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.52: 3379 107.52 - 114.68: 66723 114.68 - 121.84: 18193 121.84 - 129.00: 9336 129.00 - 136.16: 145 Bond angle restraints: 97776 Sorted by residual: angle pdb=" N ALA F 151 " pdb=" CA ALA F 151 " pdb=" C ALA F 151 " ideal model delta sigma weight residual 111.24 119.65 -8.41 1.38e+00 5.25e-01 3.71e+01 angle pdb=" N SER E 266 " pdb=" CA SER E 266 " pdb=" C SER E 266 " ideal model delta sigma weight residual 109.72 115.67 -5.95 1.60e+00 3.91e-01 1.38e+01 angle pdb=" N GLY F 265 " pdb=" CA GLY F 265 " pdb=" C GLY F 265 " ideal model delta sigma weight residual 113.18 104.69 8.49 2.37e+00 1.78e-01 1.28e+01 angle pdb=" N GLU F 150 " pdb=" CA GLU F 150 " pdb=" C GLU F 150 " ideal model delta sigma weight residual 108.17 114.49 -6.32 1.85e+00 2.92e-01 1.17e+01 angle pdb=" CA GLN D 233 " pdb=" C GLN D 233 " pdb=" O GLN D 233 " ideal model delta sigma weight residual 121.84 117.89 3.95 1.16e+00 7.43e-01 1.16e+01 ... (remaining 97771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 22674 17.85 - 35.70: 1760 35.70 - 53.55: 446 53.55 - 71.40: 152 71.40 - 89.25: 9 Dihedral angle restraints: 25041 sinusoidal: 14148 harmonic: 10893 Sorted by residual: dihedral pdb=" CD ARG D 307 " pdb=" NE ARG D 307 " pdb=" CZ ARG D 307 " pdb=" NH1 ARG D 307 " ideal model delta sinusoidal sigma weight residual 0.00 32.12 -32.12 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CA ASP N 18 " pdb=" CB ASP N 18 " pdb=" CG ASP N 18 " pdb=" OD1 ASP N 18 " ideal model delta sinusoidal sigma weight residual -30.00 -89.43 59.43 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP H 18 " pdb=" CB ASP H 18 " pdb=" CG ASP H 18 " pdb=" OD1 ASP H 18 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 25038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2865 0.034 - 0.067: 863 0.067 - 0.101: 324 0.101 - 0.134: 172 0.134 - 0.168: 19 Chirality restraints: 4243 Sorted by residual: chirality pdb=" CA LEU D 236 " pdb=" N LEU D 236 " pdb=" C LEU D 236 " pdb=" CB LEU D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ILE F 301 " pdb=" N ILE F 301 " pdb=" C ILE F 301 " pdb=" CB ILE F 301 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA ILE E 301 " pdb=" N ILE E 301 " pdb=" C ILE E 301 " pdb=" CB ILE E 301 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 4240 not shown) Planarity restraints: 8002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 307 " 0.600 9.50e-02 1.11e+02 2.00e-01 4.23e+01 pdb=" NE ARG D 307 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 307 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 307 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 307 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG D 307 " -0.011 2.00e-02 2.50e+03 pdb="HH12 ARG D 307 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG D 307 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG D 307 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 123 " -0.029 2.00e-02 2.50e+03 5.87e-02 3.45e+01 pdb=" C SER E 123 " 0.102 2.00e-02 2.50e+03 pdb=" O SER E 123 " -0.038 2.00e-02 2.50e+03 pdb=" N GLY E 124 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.325 9.50e-02 1.11e+02 1.08e-01 1.24e+01 pdb=" NE ARG A 98 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.007 2.00e-02 2.50e+03 ... (remaining 7999 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 341 2.02 - 2.67: 79031 2.67 - 3.31: 151010 3.31 - 3.96: 191279 3.96 - 4.60: 301741 Nonbonded interactions: 723402 Sorted by model distance: nonbonded pdb=" HH TYR F 96 " pdb=" O ARG F 178 " model vdw 1.379 1.850 nonbonded pdb=" O GLU B 263 " pdb=" HG1 THR B 264 " model vdw 1.450 1.850 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.463 1.850 nonbonded pdb=" HZ3 LYS F 125 " pdb=" O1B ADP F 600 " model vdw 1.493 1.850 nonbonded pdb=" O MET M 5 " pdb=" HG SER N 21 " model vdw 1.515 1.850 ... (remaining 723397 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' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'B' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'C' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'D' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'E' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'F' and (resid 65 through 192 or resid 201 through 227 or resid 233 throu \ gh 259 or (resid 260 and (name N or name CA or name C or name O or name CB or na \ me CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or na \ me HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 261 through 41 \ 3)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = (chain 'K' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 192 through 193)) selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.580 Extract box with map and model: 3.680 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 125.440 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.160 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.003 0.040 27027 Z= 0.214 Angle : 0.675 9.272 36525 Z= 0.374 Chirality : 0.043 0.168 4243 Planarity : 0.006 0.257 4723 Dihedral : 11.800 89.245 10275 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -2.43 (0.12), residues: 3382 helix: -1.94 (0.11), residues: 1386 sheet: -1.20 (0.20), residues: 496 loop : -1.23 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 122 PHE 0.025 0.001 PHE H 17 TYR 0.016 0.001 TYR F 96 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 881 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 881 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LEU cc_start: 0.8625 (mt) cc_final: 0.8323 (mp) REVERT: A 317 LEU cc_start: 0.7647 (mt) cc_final: 0.6915 (tp) REVERT: C 75 ASP cc_start: 0.7866 (t70) cc_final: 0.7424 (t0) REVERT: C 115 ILE cc_start: 0.9286 (mt) cc_final: 0.9022 (mp) REVERT: C 294 ASP cc_start: 0.8410 (m-30) cc_final: 0.7751 (m-30) REVERT: C 384 MET cc_start: 0.8808 (mtm) cc_final: 0.8339 (ttm) REVERT: C 400 GLU cc_start: 0.8373 (tt0) cc_final: 0.8132 (tm-30) REVERT: D 201 ASP cc_start: 0.9092 (m-30) cc_final: 0.8605 (p0) REVERT: E 93 TYR cc_start: 0.8203 (t80) cc_final: 0.7902 (t80) REVERT: E 106 ASN cc_start: 0.7433 (m110) cc_final: 0.7206 (m110) REVERT: E 144 ASP cc_start: 0.7989 (t0) cc_final: 0.7365 (t0) REVERT: E 170 ASP cc_start: 0.8023 (m-30) cc_final: 0.7620 (t0) REVERT: E 245 PHE cc_start: 0.9024 (m-80) cc_final: 0.8663 (m-80) REVERT: E 385 TYR cc_start: 0.8508 (t80) cc_final: 0.8280 (t80) REVERT: F 86 LYS cc_start: 0.8896 (mttt) cc_final: 0.8688 (mmmt) REVERT: H 37 ASP cc_start: 0.8564 (p0) cc_final: 0.8135 (p0) REVERT: H 43 ILE cc_start: 0.9131 (mt) cc_final: 0.8722 (mm) REVERT: H 56 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8526 (mm-30) REVERT: H 60 TYR cc_start: 0.8557 (m-80) cc_final: 0.8268 (m-80) REVERT: H 64 ASN cc_start: 0.8004 (t0) cc_final: 0.7732 (t0) REVERT: I 25 LYS cc_start: 0.9192 (tttm) cc_final: 0.8877 (ttpp) REVERT: I 31 LEU cc_start: 0.9028 (tt) cc_final: 0.8819 (tp) REVERT: I 63 ILE cc_start: 0.9126 (mt) cc_final: 0.8910 (tt) REVERT: I 64 ASN cc_start: 0.9244 (t0) cc_final: 0.8909 (p0) REVERT: I 77 TYR cc_start: 0.8855 (t80) cc_final: 0.8625 (t80) REVERT: I 86 ASP cc_start: 0.8188 (m-30) cc_final: 0.7848 (m-30) REVERT: I 108 LYS cc_start: 0.9091 (tttt) cc_final: 0.8821 (mmmt) REVERT: I 120 MET cc_start: 0.8062 (ttp) cc_final: 0.7833 (tmm) REVERT: I 153 MET cc_start: 0.9333 (mmm) cc_final: 0.9111 (tpp) REVERT: J 145 VAL cc_start: 0.9326 (t) cc_final: 0.9058 (p) REVERT: K 18 ASP cc_start: 0.8631 (p0) cc_final: 0.8354 (p0) REVERT: K 43 ILE cc_start: 0.9382 (mt) cc_final: 0.8712 (mm) REVERT: K 84 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8372 (mmtm) REVERT: K 98 MET cc_start: 0.8328 (tpp) cc_final: 0.8123 (tpp) REVERT: K 121 ILE cc_start: 0.9178 (pt) cc_final: 0.8972 (mp) REVERT: K 141 GLU cc_start: 0.8898 (tp30) cc_final: 0.8657 (tp30) REVERT: K 146 LYS cc_start: 0.8666 (tttt) cc_final: 0.8409 (ttmt) REVERT: K 149 MET cc_start: 0.8746 (mmm) cc_final: 0.8397 (mmm) REVERT: L 37 ASP cc_start: 0.8601 (p0) cc_final: 0.8333 (p0) REVERT: L 49 PHE cc_start: 0.8990 (t80) cc_final: 0.8379 (t80) REVERT: L 78 ASP cc_start: 0.8864 (m-30) cc_final: 0.8330 (m-30) REVERT: L 87 VAL cc_start: 0.9553 (t) cc_final: 0.9049 (m) REVERT: L 136 GLU cc_start: 0.8894 (tt0) cc_final: 0.8692 (tm-30) REVERT: L 149 MET cc_start: 0.8625 (mmm) cc_final: 0.8401 (ttp) REVERT: L 171 ASP cc_start: 0.8643 (m-30) cc_final: 0.8320 (t0) REVERT: L 173 PHE cc_start: 0.8522 (m-80) cc_final: 0.7821 (m-10) REVERT: M 18 ASP cc_start: 0.8776 (p0) cc_final: 0.8371 (p0) REVERT: M 43 ILE cc_start: 0.9370 (mt) cc_final: 0.8980 (mm) REVERT: M 60 TYR cc_start: 0.8545 (m-80) cc_final: 0.7871 (m-80) REVERT: M 120 MET cc_start: 0.7753 (ttp) cc_final: 0.7142 (tmm) REVERT: M 165 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8632 (mt-10) REVERT: N 41 ASN cc_start: 0.8688 (t0) cc_final: 0.8237 (t0) REVERT: N 98 MET cc_start: 0.7362 (tpp) cc_final: 0.7137 (tpp) REVERT: N 153 MET cc_start: 0.9255 (mmm) cc_final: 0.8899 (mmm) outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 0.8043 time to fit residues: 1069.3798 Evaluate side-chains 506 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 162 optimal weight: 0.2980 chunk 198 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 195 ASN B 324 GLN F 208 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN I 41 ASN J 41 ASN K 34 GLN K 41 ASN K 116 ASN K 138 HIS L 41 ASN L 163 GLN M 9 GLN M 41 ASN N 116 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27027 Z= 0.240 Angle : 0.576 7.136 36525 Z= 0.308 Chirality : 0.040 0.180 4243 Planarity : 0.004 0.062 4723 Dihedral : 5.415 51.765 3783 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3382 helix: 0.11 (0.13), residues: 1479 sheet: -0.83 (0.22), residues: 462 loop : -0.99 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 73 PHE 0.018 0.001 PHE J 101 TYR 0.019 0.001 TYR F 153 ARG 0.008 0.001 ARG E 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 586 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 585 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.9607 (m-30) cc_final: 0.9391 (m-30) REVERT: A 317 LEU cc_start: 0.7752 (mt) cc_final: 0.7298 (tp) REVERT: B 212 LEU cc_start: 0.9117 (mt) cc_final: 0.8842 (mt) REVERT: C 75 ASP cc_start: 0.8072 (t70) cc_final: 0.7796 (t0) REVERT: C 115 ILE cc_start: 0.9306 (mt) cc_final: 0.9072 (mm) REVERT: C 255 ASP cc_start: 0.8162 (p0) cc_final: 0.7960 (p0) REVERT: C 384 MET cc_start: 0.9008 (mtm) cc_final: 0.8543 (ttm) REVERT: C 400 GLU cc_start: 0.8410 (tt0) cc_final: 0.8136 (tm-30) REVERT: D 115 ILE cc_start: 0.9091 (mt) cc_final: 0.8786 (mm) REVERT: D 293 GLU cc_start: 0.8546 (pm20) cc_final: 0.8057 (pm20) REVERT: D 294 ASP cc_start: 0.8237 (m-30) cc_final: 0.7147 (m-30) REVERT: D 377 GLU cc_start: 0.8294 (tp30) cc_final: 0.7956 (tp30) REVERT: E 93 TYR cc_start: 0.8380 (t80) cc_final: 0.7913 (t80) REVERT: E 170 ASP cc_start: 0.8246 (m-30) cc_final: 0.7732 (t0) REVERT: E 175 LYS cc_start: 0.9264 (tttt) cc_final: 0.9021 (ttpt) REVERT: F 182 TYR cc_start: 0.8880 (t80) cc_final: 0.8528 (t80) REVERT: F 202 VAL cc_start: 0.8764 (m) cc_final: 0.8381 (p) REVERT: F 294 ASP cc_start: 0.8786 (m-30) cc_final: 0.7780 (m-30) REVERT: H 37 ASP cc_start: 0.8350 (p0) cc_final: 0.7897 (p0) REVERT: H 54 ASN cc_start: 0.8171 (t0) cc_final: 0.7516 (t0) REVERT: H 56 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8716 (mm-30) REVERT: H 181 GLU cc_start: 0.8845 (tt0) cc_final: 0.8604 (tm-30) REVERT: I 53 GLU cc_start: 0.8944 (tp30) cc_final: 0.8718 (tp30) REVERT: J 64 ASN cc_start: 0.9619 (t0) cc_final: 0.9376 (t0) REVERT: K 18 ASP cc_start: 0.8805 (p0) cc_final: 0.8522 (p0) REVERT: K 74 MET cc_start: 0.8845 (mmm) cc_final: 0.8493 (mmp) REVERT: K 84 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8556 (mmtm) REVERT: K 149 MET cc_start: 0.8683 (mmm) cc_final: 0.8408 (mmm) REVERT: L 120 MET cc_start: 0.8521 (ttp) cc_final: 0.7902 (tmm) REVERT: L 173 PHE cc_start: 0.8481 (m-80) cc_final: 0.8263 (m-80) REVERT: M 37 ASP cc_start: 0.8609 (p0) cc_final: 0.7934 (p0) REVERT: M 60 TYR cc_start: 0.8583 (m-80) cc_final: 0.7905 (m-80) REVERT: N 41 ASN cc_start: 0.8829 (t0) cc_final: 0.8559 (t0) REVERT: N 60 TYR cc_start: 0.8665 (m-80) cc_final: 0.8214 (m-80) REVERT: N 153 MET cc_start: 0.9258 (mmm) cc_final: 0.8950 (mmm) outliers start: 1 outliers final: 0 residues processed: 586 average time/residue: 0.7567 time to fit residues: 691.2042 Evaluate side-chains 430 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 334 optimal weight: 0.3980 chunk 275 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN K 41 ASN L 163 GLN M 9 GLN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27027 Z= 0.186 Angle : 0.488 5.714 36525 Z= 0.252 Chirality : 0.039 0.152 4243 Planarity : 0.003 0.067 4723 Dihedral : 5.219 54.132 3783 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3382 helix: 0.55 (0.13), residues: 1483 sheet: -0.65 (0.23), residues: 467 loop : -0.84 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 260 PHE 0.022 0.001 PHE E 270 TYR 0.015 0.001 TYR K 128 ARG 0.006 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 520 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7590 (mt) cc_final: 0.7177 (tp) REVERT: A 337 TYR cc_start: 0.8078 (m-10) cc_final: 0.6931 (m-10) REVERT: A 363 MET cc_start: 0.8547 (tpp) cc_final: 0.8291 (tpp) REVERT: B 163 GLN cc_start: 0.8495 (tt0) cc_final: 0.7888 (tm-30) REVERT: B 212 LEU cc_start: 0.9120 (mt) cc_final: 0.8824 (mt) REVERT: B 399 ASP cc_start: 0.8465 (m-30) cc_final: 0.8254 (m-30) REVERT: C 384 MET cc_start: 0.8974 (mtm) cc_final: 0.8476 (ttm) REVERT: C 400 GLU cc_start: 0.8393 (tt0) cc_final: 0.8087 (tm-30) REVERT: D 115 ILE cc_start: 0.9071 (mt) cc_final: 0.8780 (mm) REVERT: D 356 ASP cc_start: 0.8431 (m-30) cc_final: 0.8053 (t0) REVERT: D 377 GLU cc_start: 0.8342 (tp30) cc_final: 0.7944 (tp30) REVERT: E 170 ASP cc_start: 0.8294 (m-30) cc_final: 0.7695 (t0) REVERT: E 175 LYS cc_start: 0.9302 (tttt) cc_final: 0.9053 (ttpt) REVERT: F 182 TYR cc_start: 0.8940 (t80) cc_final: 0.8631 (t80) REVERT: F 218 THR cc_start: 0.8412 (p) cc_final: 0.7860 (p) REVERT: F 270 PHE cc_start: 0.8006 (m-80) cc_final: 0.7766 (m-80) REVERT: F 274 VAL cc_start: 0.7784 (p) cc_final: 0.7273 (p) REVERT: H 37 ASP cc_start: 0.8411 (p0) cc_final: 0.7853 (p0) REVERT: H 54 ASN cc_start: 0.8070 (t0) cc_final: 0.7503 (t0) REVERT: H 56 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8718 (mm-30) REVERT: I 53 GLU cc_start: 0.8993 (tp30) cc_final: 0.8772 (tp30) REVERT: I 120 MET cc_start: 0.8155 (ttp) cc_final: 0.7781 (tmm) REVERT: K 74 MET cc_start: 0.8872 (mmm) cc_final: 0.8541 (mmp) REVERT: K 120 MET cc_start: 0.8276 (tmm) cc_final: 0.7982 (tmm) REVERT: K 149 MET cc_start: 0.8741 (mmm) cc_final: 0.8440 (mmm) REVERT: L 120 MET cc_start: 0.8563 (ttp) cc_final: 0.7868 (tmm) REVERT: L 173 PHE cc_start: 0.8462 (m-80) cc_final: 0.8257 (m-80) REVERT: M 18 ASP cc_start: 0.8940 (p0) cc_final: 0.8698 (p0) REVERT: M 24 LEU cc_start: 0.9125 (tt) cc_final: 0.8913 (tt) REVERT: M 37 ASP cc_start: 0.8612 (p0) cc_final: 0.7910 (p0) REVERT: M 60 TYR cc_start: 0.8628 (m-80) cc_final: 0.8064 (m-80) REVERT: M 74 MET cc_start: 0.9379 (mmm) cc_final: 0.8974 (mmm) REVERT: N 41 ASN cc_start: 0.8734 (t0) cc_final: 0.8404 (t0) REVERT: N 153 MET cc_start: 0.9266 (mmm) cc_final: 0.8977 (mmm) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.6804 time to fit residues: 562.8913 Evaluate side-chains 406 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 9.9990 chunk 232 optimal weight: 0.0970 chunk 160 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 328 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN F 232 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN L 150 ASN L 163 GLN M 9 GLN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27027 Z= 0.190 Angle : 0.477 5.651 36525 Z= 0.246 Chirality : 0.039 0.150 4243 Planarity : 0.003 0.040 4723 Dihedral : 5.201 56.513 3783 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.07 % Allowed : 1.12 % Favored : 98.81 % 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: -0.11 (0.14), residues: 3382 helix: 0.75 (0.13), residues: 1485 sheet: -0.52 (0.22), residues: 491 loop : -0.70 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 73 PHE 0.010 0.001 PHE I 101 TYR 0.017 0.001 TYR F 171 ARG 0.008 0.000 ARG K 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 489 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLN cc_start: 0.8481 (tt0) cc_final: 0.7691 (tm-30) REVERT: B 212 LEU cc_start: 0.9124 (mt) cc_final: 0.8874 (mt) REVERT: C 384 MET cc_start: 0.9014 (mtm) cc_final: 0.8523 (ttm) REVERT: C 400 GLU cc_start: 0.8434 (tt0) cc_final: 0.8071 (tm-30) REVERT: D 115 ILE cc_start: 0.9012 (mt) cc_final: 0.8786 (mm) REVERT: D 356 ASP cc_start: 0.8470 (m-30) cc_final: 0.8113 (t0) REVERT: D 377 GLU cc_start: 0.8520 (tp30) cc_final: 0.8081 (tp30) REVERT: E 144 ASP cc_start: 0.8214 (p0) cc_final: 0.7923 (p0) REVERT: E 170 ASP cc_start: 0.8309 (m-30) cc_final: 0.7645 (t0) REVERT: E 175 LYS cc_start: 0.9315 (tttt) cc_final: 0.9074 (ttpt) REVERT: F 182 TYR cc_start: 0.8954 (t80) cc_final: 0.8651 (t80) REVERT: F 205 GLU cc_start: 0.8175 (pp20) cc_final: 0.7968 (pp20) REVERT: H 37 ASP cc_start: 0.8387 (p0) cc_final: 0.7960 (p0) REVERT: H 54 ASN cc_start: 0.8024 (t0) cc_final: 0.7461 (t0) REVERT: I 120 MET cc_start: 0.8259 (ttp) cc_final: 0.7780 (tmm) REVERT: J 60 TYR cc_start: 0.8700 (m-80) cc_final: 0.8425 (m-80) REVERT: K 120 MET cc_start: 0.8274 (tmm) cc_final: 0.7876 (tmm) REVERT: K 149 MET cc_start: 0.8811 (mmm) cc_final: 0.8414 (mmm) REVERT: L 120 MET cc_start: 0.8556 (ttp) cc_final: 0.7858 (tmm) REVERT: M 37 ASP cc_start: 0.8671 (p0) cc_final: 0.8005 (p0) REVERT: M 60 TYR cc_start: 0.8651 (m-80) cc_final: 0.8085 (m-80) REVERT: M 74 MET cc_start: 0.9396 (mmm) cc_final: 0.9025 (mmm) REVERT: N 134 ASP cc_start: 0.8886 (t0) cc_final: 0.8529 (t0) REVERT: N 153 MET cc_start: 0.9280 (mmm) cc_final: 0.8998 (mmm) outliers start: 2 outliers final: 0 residues processed: 490 average time/residue: 0.6735 time to fit residues: 531.7609 Evaluate side-chains 393 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 406 GLN C 331 ASN D 83 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 GLN J 150 ASN K 41 ASN L 163 GLN M 9 GLN M 41 ASN M 163 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 27027 Z= 0.420 Angle : 0.665 12.689 36525 Z= 0.346 Chirality : 0.042 0.235 4243 Planarity : 0.004 0.038 4723 Dihedral : 5.738 60.297 3783 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.10 % Allowed : 2.13 % Favored : 97.76 % 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: -0.80 (0.14), residues: 3382 helix: 0.11 (0.13), residues: 1506 sheet: -0.75 (0.23), residues: 460 loop : -1.04 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 260 PHE 0.033 0.002 PHE L 173 TYR 0.018 0.002 TYR F 96 ARG 0.005 0.001 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 454 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 451 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLN cc_start: 0.8590 (tt0) cc_final: 0.8064 (tm-30) REVERT: B 212 LEU cc_start: 0.9179 (mt) cc_final: 0.8933 (mt) REVERT: B 247 CYS cc_start: 0.8628 (m) cc_final: 0.8383 (m) REVERT: B 399 ASP cc_start: 0.8475 (m-30) cc_final: 0.8258 (m-30) REVERT: C 384 MET cc_start: 0.9081 (mtm) cc_final: 0.8657 (ttm) REVERT: C 400 GLU cc_start: 0.8511 (tt0) cc_final: 0.8068 (tm-30) REVERT: D 115 ILE cc_start: 0.8994 (mt) cc_final: 0.8734 (mm) REVERT: D 170 ASP cc_start: 0.8816 (t0) cc_final: 0.8613 (t0) REVERT: D 356 ASP cc_start: 0.8572 (m-30) cc_final: 0.8248 (t0) REVERT: D 366 LYS cc_start: 0.9390 (mtmt) cc_final: 0.9108 (ptpt) REVERT: D 377 GLU cc_start: 0.8693 (tp30) cc_final: 0.8299 (tp30) REVERT: E 144 ASP cc_start: 0.8517 (p0) cc_final: 0.8138 (p0) REVERT: E 175 LYS cc_start: 0.9382 (tttt) cc_final: 0.9145 (tppt) REVERT: E 384 MET cc_start: 0.8988 (mtm) cc_final: 0.8383 (mpp) REVERT: F 168 LYS cc_start: 0.9039 (tptt) cc_final: 0.8686 (tptp) REVERT: F 182 TYR cc_start: 0.8987 (t80) cc_final: 0.8647 (t80) REVERT: F 205 GLU cc_start: 0.8185 (pp20) cc_final: 0.7974 (pp20) REVERT: I 120 MET cc_start: 0.8569 (ttp) cc_final: 0.7817 (tmm) REVERT: K 113 CYS cc_start: 0.7561 (p) cc_final: 0.7322 (p) REVERT: K 120 MET cc_start: 0.8418 (tmm) cc_final: 0.7924 (tmm) REVERT: K 149 MET cc_start: 0.8918 (mmm) cc_final: 0.8621 (mmm) REVERT: L 5 MET cc_start: 0.8825 (mmp) cc_final: 0.8421 (mmm) REVERT: L 120 MET cc_start: 0.8520 (ttp) cc_final: 0.7278 (ttp) REVERT: L 171 ASP cc_start: 0.8707 (m-30) cc_final: 0.8168 (t0) REVERT: M 24 LEU cc_start: 0.9128 (tt) cc_final: 0.8902 (tt) REVERT: M 60 TYR cc_start: 0.8839 (m-80) cc_final: 0.8406 (m-80) REVERT: M 149 MET cc_start: 0.9403 (ttt) cc_final: 0.9193 (ttm) REVERT: N 153 MET cc_start: 0.9302 (mmm) cc_final: 0.8996 (mmm) outliers start: 3 outliers final: 1 residues processed: 452 average time/residue: 0.6770 time to fit residues: 494.3172 Evaluate side-chains 372 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 328 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN J 41 ASN K 41 ASN M 41 ASN ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27027 Z= 0.275 Angle : 0.534 6.435 36525 Z= 0.278 Chirality : 0.040 0.153 4243 Planarity : 0.003 0.035 4723 Dihedral : 5.721 63.405 3783 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.03 % Allowed : 0.91 % Favored : 99.06 % 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: -0.57 (0.14), residues: 3382 helix: 0.30 (0.13), residues: 1506 sheet: -0.62 (0.23), residues: 458 loop : -0.91 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 95 PHE 0.030 0.001 PHE B 245 TYR 0.016 0.001 TYR F 96 ARG 0.006 0.000 ARG E 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 CYS cc_start: 0.9302 (m) cc_final: 0.9093 (m) REVERT: B 163 GLN cc_start: 0.8581 (tt0) cc_final: 0.8101 (tm-30) REVERT: B 212 LEU cc_start: 0.9192 (mt) cc_final: 0.8959 (mt) REVERT: B 399 ASP cc_start: 0.8449 (m-30) cc_final: 0.8237 (m-30) REVERT: C 384 MET cc_start: 0.9051 (mtm) cc_final: 0.8590 (mtm) REVERT: C 400 GLU cc_start: 0.8509 (tt0) cc_final: 0.8017 (tm-30) REVERT: D 115 ILE cc_start: 0.8961 (mt) cc_final: 0.8723 (mm) REVERT: D 170 ASP cc_start: 0.8852 (t0) cc_final: 0.8491 (t0) REVERT: D 172 ASP cc_start: 0.8162 (m-30) cc_final: 0.7819 (m-30) REVERT: D 356 ASP cc_start: 0.8521 (m-30) cc_final: 0.8307 (t0) REVERT: D 366 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9059 (ptpt) REVERT: D 377 GLU cc_start: 0.8778 (tp30) cc_final: 0.8317 (tp30) REVERT: E 101 ASN cc_start: 0.8724 (m-40) cc_final: 0.8120 (t0) REVERT: E 144 ASP cc_start: 0.8451 (p0) cc_final: 0.7994 (p0) REVERT: E 247 CYS cc_start: 0.8491 (m) cc_final: 0.8286 (m) REVERT: E 384 MET cc_start: 0.8962 (mtm) cc_final: 0.8494 (mpp) REVERT: F 182 TYR cc_start: 0.8968 (t80) cc_final: 0.8497 (t80) REVERT: F 205 GLU cc_start: 0.8172 (pp20) cc_final: 0.7949 (pp20) REVERT: H 41 ASN cc_start: 0.8417 (m110) cc_final: 0.8131 (m110) REVERT: I 64 ASN cc_start: 0.8998 (p0) cc_final: 0.7718 (p0) REVERT: I 120 MET cc_start: 0.8482 (ttp) cc_final: 0.7978 (tmm) REVERT: J 134 ASP cc_start: 0.9025 (m-30) cc_final: 0.8709 (p0) REVERT: K 113 CYS cc_start: 0.7594 (p) cc_final: 0.7361 (p) REVERT: K 120 MET cc_start: 0.8387 (tmm) cc_final: 0.7877 (tmm) REVERT: K 149 MET cc_start: 0.8882 (mmm) cc_final: 0.8562 (mmm) REVERT: L 37 ASP cc_start: 0.8480 (p0) cc_final: 0.8107 (p0) REVERT: L 171 ASP cc_start: 0.8606 (m-30) cc_final: 0.8378 (t0) REVERT: M 37 ASP cc_start: 0.8613 (p0) cc_final: 0.8051 (p0) REVERT: M 53 GLU cc_start: 0.8839 (tp30) cc_final: 0.8592 (tp30) REVERT: M 60 TYR cc_start: 0.8799 (m-80) cc_final: 0.8363 (m-80) REVERT: N 134 ASP cc_start: 0.8888 (t0) cc_final: 0.8492 (t0) REVERT: N 153 MET cc_start: 0.9291 (mmm) cc_final: 0.9059 (mmm) outliers start: 1 outliers final: 0 residues processed: 452 average time/residue: 0.6649 time to fit residues: 487.6041 Evaluate side-chains 379 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 327 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 41 ASN L 163 GLN M 41 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 27027 Z= 0.411 Angle : 0.630 11.503 36525 Z= 0.326 Chirality : 0.041 0.216 4243 Planarity : 0.004 0.045 4723 Dihedral : 5.817 64.217 3783 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -1.01 (0.14), residues: 3382 helix: -0.06 (0.13), residues: 1509 sheet: -0.60 (0.21), residues: 518 loop : -1.28 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 73 PHE 0.021 0.002 PHE D 298 TYR 0.018 0.002 TYR E 93 ARG 0.005 0.001 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7472 (tp) cc_final: 0.7075 (tp) REVERT: A 342 ASN cc_start: 0.8467 (m-40) cc_final: 0.8233 (m110) REVERT: B 163 GLN cc_start: 0.8597 (tt0) cc_final: 0.8172 (tm-30) REVERT: B 212 LEU cc_start: 0.9215 (mt) cc_final: 0.8984 (mt) REVERT: B 399 ASP cc_start: 0.8604 (m-30) cc_final: 0.8381 (m-30) REVERT: C 384 MET cc_start: 0.9081 (mtm) cc_final: 0.8674 (mtm) REVERT: C 400 GLU cc_start: 0.8559 (tt0) cc_final: 0.7998 (tm-30) REVERT: D 115 ILE cc_start: 0.8994 (mt) cc_final: 0.8772 (mm) REVERT: D 366 LYS cc_start: 0.9383 (mtmt) cc_final: 0.9089 (ptpt) REVERT: D 377 GLU cc_start: 0.8778 (tp30) cc_final: 0.8434 (tp30) REVERT: E 144 ASP cc_start: 0.8496 (p0) cc_final: 0.7982 (p0) REVERT: E 247 CYS cc_start: 0.8521 (m) cc_final: 0.8286 (m) REVERT: E 384 MET cc_start: 0.8995 (mtm) cc_final: 0.8545 (mpp) REVERT: F 202 VAL cc_start: 0.8786 (m) cc_final: 0.8163 (t) REVERT: H 41 ASN cc_start: 0.8513 (m110) cc_final: 0.8236 (m110) REVERT: H 80 MET cc_start: 0.9006 (mtp) cc_final: 0.8756 (ttp) REVERT: I 101 PHE cc_start: 0.9398 (t80) cc_final: 0.9048 (t80) REVERT: I 120 MET cc_start: 0.8635 (ttp) cc_final: 0.8032 (tmm) REVERT: K 113 CYS cc_start: 0.7741 (p) cc_final: 0.7498 (p) REVERT: K 120 MET cc_start: 0.8440 (tmm) cc_final: 0.7942 (tmm) REVERT: L 37 ASP cc_start: 0.8494 (p0) cc_final: 0.8170 (p0) REVERT: L 171 ASP cc_start: 0.8623 (m-30) cc_final: 0.8370 (t0) REVERT: M 37 ASP cc_start: 0.8665 (p0) cc_final: 0.8122 (p0) REVERT: M 53 GLU cc_start: 0.8845 (tp30) cc_final: 0.8600 (tp30) REVERT: M 60 TYR cc_start: 0.8842 (m-80) cc_final: 0.8437 (m-10) REVERT: M 149 MET cc_start: 0.9409 (ttt) cc_final: 0.9193 (ttm) REVERT: N 134 ASP cc_start: 0.8914 (t0) cc_final: 0.8524 (t0) REVERT: N 153 MET cc_start: 0.9292 (mmm) cc_final: 0.9068 (mmm) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.6955 time to fit residues: 495.0727 Evaluate side-chains 365 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 257 optimal weight: 0.5980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 41 ASN M 41 ASN ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27027 Z= 0.178 Angle : 0.484 5.825 36525 Z= 0.249 Chirality : 0.040 0.159 4243 Planarity : 0.003 0.046 4723 Dihedral : 5.599 66.175 3783 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3382 helix: 0.51 (0.13), residues: 1505 sheet: -0.44 (0.22), residues: 518 loop : -0.97 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 95 PHE 0.016 0.001 PHE A 235 TYR 0.016 0.001 TYR F 96 ARG 0.004 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 457 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 CYS cc_start: 0.9406 (m) cc_final: 0.9194 (m) REVERT: B 163 GLN cc_start: 0.8541 (tt0) cc_final: 0.8168 (tm-30) REVERT: B 212 LEU cc_start: 0.9177 (mt) cc_final: 0.8960 (mt) REVERT: C 384 MET cc_start: 0.9032 (mtm) cc_final: 0.8616 (mtm) REVERT: C 400 GLU cc_start: 0.8440 (tt0) cc_final: 0.7790 (tm-30) REVERT: D 115 ILE cc_start: 0.8929 (mt) cc_final: 0.8702 (mm) REVERT: D 188 LYS cc_start: 0.9040 (tptt) cc_final: 0.8817 (tptm) REVERT: D 366 LYS cc_start: 0.9362 (mtmt) cc_final: 0.9058 (ptpt) REVERT: D 377 GLU cc_start: 0.8726 (tp30) cc_final: 0.8389 (tp30) REVERT: E 144 ASP cc_start: 0.8427 (p0) cc_final: 0.7941 (p0) REVERT: E 247 CYS cc_start: 0.8518 (m) cc_final: 0.8237 (m) REVERT: F 182 TYR cc_start: 0.9009 (t80) cc_final: 0.8624 (t80) REVERT: F 202 VAL cc_start: 0.8792 (m) cc_final: 0.8547 (p) REVERT: H 41 ASN cc_start: 0.8443 (m110) cc_final: 0.8132 (m110) REVERT: I 5 MET cc_start: 0.8278 (mmm) cc_final: 0.7707 (mmm) REVERT: I 80 MET cc_start: 0.8981 (mtm) cc_final: 0.8744 (mpp) REVERT: I 120 MET cc_start: 0.8487 (ttp) cc_final: 0.7995 (tmm) REVERT: J 98 MET cc_start: 0.7553 (tpp) cc_final: 0.7323 (tpp) REVERT: J 101 PHE cc_start: 0.9113 (t80) cc_final: 0.8730 (t80) REVERT: J 134 ASP cc_start: 0.9056 (m-30) cc_final: 0.8748 (p0) REVERT: J 144 LYS cc_start: 0.9250 (mmtt) cc_final: 0.9037 (mmmt) REVERT: K 113 CYS cc_start: 0.7638 (p) cc_final: 0.7394 (p) REVERT: K 120 MET cc_start: 0.8401 (tmm) cc_final: 0.7890 (tmm) REVERT: L 5 MET cc_start: 0.8615 (mmp) cc_final: 0.8264 (mmm) REVERT: L 37 ASP cc_start: 0.8475 (p0) cc_final: 0.8107 (p0) REVERT: M 37 ASP cc_start: 0.8590 (p0) cc_final: 0.8050 (p0) REVERT: M 53 GLU cc_start: 0.8811 (tp30) cc_final: 0.8595 (tp30) REVERT: M 60 TYR cc_start: 0.8845 (m-80) cc_final: 0.8417 (m-10) REVERT: M 113 CYS cc_start: 0.7682 (p) cc_final: 0.7461 (p) REVERT: M 149 MET cc_start: 0.9402 (ttt) cc_final: 0.9183 (ttm) REVERT: N 134 ASP cc_start: 0.8944 (t0) cc_final: 0.8541 (t0) REVERT: N 153 MET cc_start: 0.9255 (mmm) cc_final: 0.9013 (mmm) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.6932 time to fit residues: 509.4574 Evaluate side-chains 368 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 288 optimal weight: 10.0000 chunk 304 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** J 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN M 41 ASN ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 27027 Z= 0.296 Angle : 0.549 8.808 36525 Z= 0.283 Chirality : 0.040 0.201 4243 Planarity : 0.003 0.057 4723 Dihedral : 5.664 65.974 3783 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.62 (0.14), residues: 3382 helix: 0.32 (0.13), residues: 1508 sheet: -0.54 (0.21), residues: 530 loop : -1.08 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 73 PHE 0.017 0.001 PHE D 298 TYR 0.017 0.002 TYR F 96 ARG 0.004 0.000 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 CYS cc_start: 0.9419 (m) cc_final: 0.9202 (m) REVERT: B 163 GLN cc_start: 0.8552 (tt0) cc_final: 0.8200 (tm-30) REVERT: B 212 LEU cc_start: 0.9192 (mt) cc_final: 0.8985 (mt) REVERT: B 399 ASP cc_start: 0.8557 (m-30) cc_final: 0.8324 (m-30) REVERT: C 384 MET cc_start: 0.9047 (mtm) cc_final: 0.8661 (mtm) REVERT: C 400 GLU cc_start: 0.8511 (tt0) cc_final: 0.7960 (tm-30) REVERT: D 115 ILE cc_start: 0.8972 (mt) cc_final: 0.8756 (mm) REVERT: D 188 LYS cc_start: 0.9049 (tptt) cc_final: 0.8838 (tptm) REVERT: D 366 LYS cc_start: 0.9371 (mtmt) cc_final: 0.9079 (ptpt) REVERT: D 377 GLU cc_start: 0.8822 (tp30) cc_final: 0.8449 (tp30) REVERT: E 144 ASP cc_start: 0.8484 (p0) cc_final: 0.7945 (p0) REVERT: E 247 CYS cc_start: 0.8488 (m) cc_final: 0.8257 (m) REVERT: H 41 ASN cc_start: 0.8463 (m110) cc_final: 0.8198 (m110) REVERT: I 5 MET cc_start: 0.8260 (mmm) cc_final: 0.7756 (mmm) REVERT: I 80 MET cc_start: 0.8948 (mtm) cc_final: 0.8664 (mpp) REVERT: I 120 MET cc_start: 0.8541 (ttp) cc_final: 0.8059 (tmm) REVERT: J 134 ASP cc_start: 0.8990 (m-30) cc_final: 0.8662 (p0) REVERT: J 144 LYS cc_start: 0.9282 (mmtt) cc_final: 0.9036 (mmmt) REVERT: K 113 CYS cc_start: 0.7745 (p) cc_final: 0.7497 (p) REVERT: K 120 MET cc_start: 0.8433 (tmm) cc_final: 0.7921 (tmm) REVERT: L 37 ASP cc_start: 0.8505 (p0) cc_final: 0.8180 (p0) REVERT: L 113 CYS cc_start: 0.7342 (p) cc_final: 0.7132 (p) REVERT: M 37 ASP cc_start: 0.8618 (p0) cc_final: 0.8074 (p0) REVERT: M 60 TYR cc_start: 0.8881 (m-80) cc_final: 0.8485 (m-10) REVERT: M 113 CYS cc_start: 0.7683 (p) cc_final: 0.7478 (p) REVERT: M 149 MET cc_start: 0.9409 (ttt) cc_final: 0.9184 (ttm) REVERT: N 134 ASP cc_start: 0.8924 (t0) cc_final: 0.8512 (t0) REVERT: N 153 MET cc_start: 0.9309 (mmm) cc_final: 0.9044 (mmm) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.6976 time to fit residues: 489.8528 Evaluate side-chains 351 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 20.0000 chunk 322 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 153 optimal weight: 0.3980 chunk 224 optimal weight: 2.9990 chunk 338 optimal weight: 0.6980 chunk 311 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 165 optimal weight: 0.0370 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN F 342 ASN I 41 ASN K 41 ASN M 41 ASN N 41 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27027 Z= 0.134 Angle : 0.468 8.173 36525 Z= 0.239 Chirality : 0.040 0.175 4243 Planarity : 0.003 0.044 4723 Dihedral : 5.471 67.717 3783 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % 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: -0.04 (0.14), residues: 3382 helix: 0.86 (0.13), residues: 1505 sheet: -0.28 (0.22), residues: 528 loop : -0.85 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 230 PHE 0.021 0.001 PHE N 101 TYR 0.015 0.001 TYR F 96 ARG 0.006 0.000 ARG K 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 457 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 CYS cc_start: 0.9392 (m) cc_final: 0.9159 (m) REVERT: A 317 LEU cc_start: 0.7771 (mt) cc_final: 0.7267 (tp) REVERT: B 163 GLN cc_start: 0.8561 (tt0) cc_final: 0.8195 (tm-30) REVERT: C 384 MET cc_start: 0.8984 (mtm) cc_final: 0.8568 (ttm) REVERT: C 400 GLU cc_start: 0.8455 (tt0) cc_final: 0.7790 (tm-30) REVERT: D 115 ILE cc_start: 0.8900 (mt) cc_final: 0.8674 (mm) REVERT: D 188 LYS cc_start: 0.8992 (tptt) cc_final: 0.8769 (tptm) REVERT: D 363 MET cc_start: 0.8586 (mtt) cc_final: 0.7920 (mtt) REVERT: D 377 GLU cc_start: 0.8766 (tp30) cc_final: 0.8335 (tp30) REVERT: E 144 ASP cc_start: 0.8414 (p0) cc_final: 0.7891 (p0) REVERT: E 247 CYS cc_start: 0.8488 (m) cc_final: 0.8229 (m) REVERT: F 202 VAL cc_start: 0.9060 (p) cc_final: 0.8676 (t) REVERT: H 41 ASN cc_start: 0.8397 (m110) cc_final: 0.8102 (m110) REVERT: I 5 MET cc_start: 0.8234 (mmm) cc_final: 0.7762 (mmm) REVERT: I 64 ASN cc_start: 0.8250 (p0) cc_final: 0.7836 (p0) REVERT: I 80 MET cc_start: 0.8957 (mtm) cc_final: 0.8686 (mpp) REVERT: I 120 MET cc_start: 0.8331 (ttp) cc_final: 0.7976 (tmm) REVERT: J 101 PHE cc_start: 0.8764 (t80) cc_final: 0.8560 (t80) REVERT: J 134 ASP cc_start: 0.9032 (m-30) cc_final: 0.8639 (p0) REVERT: J 144 LYS cc_start: 0.9279 (mmtt) cc_final: 0.9048 (mmmt) REVERT: K 113 CYS cc_start: 0.7778 (p) cc_final: 0.7521 (p) REVERT: K 120 MET cc_start: 0.8360 (tmm) cc_final: 0.7865 (tmm) REVERT: L 37 ASP cc_start: 0.8496 (p0) cc_final: 0.8126 (p0) REVERT: L 113 CYS cc_start: 0.7232 (p) cc_final: 0.7024 (p) REVERT: L 120 MET cc_start: 0.7833 (ttp) cc_final: 0.7254 (ttp) REVERT: L 171 ASP cc_start: 0.6868 (t0) cc_final: 0.6369 (t0) REVERT: M 37 ASP cc_start: 0.8567 (p0) cc_final: 0.8049 (p0) REVERT: M 60 TYR cc_start: 0.8863 (m-80) cc_final: 0.8453 (m-80) REVERT: M 113 CYS cc_start: 0.7673 (p) cc_final: 0.7418 (p) REVERT: M 149 MET cc_start: 0.9413 (ttt) cc_final: 0.9183 (ttm) REVERT: N 74 MET cc_start: 0.9488 (mmp) cc_final: 0.9211 (mmp) REVERT: N 134 ASP cc_start: 0.8933 (t0) cc_final: 0.8516 (t0) REVERT: N 149 MET cc_start: 0.8845 (tpp) cc_final: 0.8290 (ttt) REVERT: N 153 MET cc_start: 0.9251 (mmm) cc_final: 0.8989 (mmm) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.7104 time to fit residues: 522.8403 Evaluate side-chains 370 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 41 ASN M 41 ASN N 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.086072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.066217 restraints weight = 255537.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069647 restraints weight = 117662.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071922 restraints weight = 70589.287| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27027 Z= 0.166 Angle : 0.470 8.269 36525 Z= 0.240 Chirality : 0.039 0.169 4243 Planarity : 0.003 0.041 4723 Dihedral : 5.383 77.216 3783 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3382 helix: 0.95 (0.13), residues: 1517 sheet: -0.25 (0.22), residues: 530 loop : -0.77 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 230 PHE 0.014 0.001 PHE A 245 TYR 0.016 0.001 TYR F 96 ARG 0.006 0.000 ARG K 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9821.26 seconds wall clock time: 170 minutes 49.14 seconds (10249.14 seconds total)