Starting phenix.real_space_refine on Thu Dec 7 16:17:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/12_2023/6pos_20418_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/12_2023/6pos_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_20418/12_2023/6pos_20418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/12_2023/6pos_20418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/12_2023/6pos_20418_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pos_20418/12_2023/6pos_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-1.21rc1-5172/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: 18.04, per 1000 atoms: 0.34 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: 31.56 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: 5.75 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: 16.60 Time building geometry restraints manager: 33.35 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: 22295 17.85 - 35.70: 1610 35.70 - 53.55: 253 53.55 - 71.40: 37 71.40 - 89.25: 9 Dihedral angle restraints: 24204 sinusoidal: 13311 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 24201 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: 0.590 Extract box with map and model: 3.630 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 124.250 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.270 ------------------------------------------------------------------------------- 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 : 3.173 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 outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 0.8025 time to fit residues: 1066.7005 Evaluate side-chains 486 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 3.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8963 ------------------------------------------------------------------------------- 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: 4.9990 chunk 257 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 266 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 H 64 ASN H 116 ASN I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 GLN 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 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27027 Z= 0.277 Angle : 0.601 7.991 36525 Z= 0.320 Chirality : 0.040 0.160 4243 Planarity : 0.004 0.069 4723 Dihedral : 5.420 52.070 3783 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.10 % Allowed : 1.85 % Favored : 98.04 % 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: -0.84 (0.14), residues: 3382 helix: 0.09 (0.13), residues: 1485 sheet: -0.83 (0.22), residues: 462 loop : -1.03 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 73 PHE 0.017 0.001 PHE J 101 TYR 0.021 0.002 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 563 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 560 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: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 562 average time/residue: 0.7618 time to fit residues: 669.6136 Evaluate side-chains 405 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9477 ------------------------------------------------------------------------------- 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: 10.0000 chunk 95 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 chunk 334 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 116 ASN I 41 ASN I 46 GLN K 34 GLN K 41 ASN L 150 ASN L 163 GLN M 9 GLN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN N 129 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27027 Z= 0.348 Angle : 0.605 9.520 36525 Z= 0.315 Chirality : 0.041 0.177 4243 Planarity : 0.004 0.044 4723 Dihedral : 5.429 56.585 3783 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3382 helix: 0.28 (0.13), residues: 1495 sheet: -0.86 (0.22), residues: 504 loop : -1.07 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 260 PHE 0.024 0.002 PHE E 270 TYR 0.021 0.002 TYR F 413 ARG 0.040 0.001 ARG F 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 482 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 3.153 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 outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.7053 time to fit residues: 538.0560 Evaluate side-chains 376 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 3.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8679 ------------------------------------------------------------------------------- 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: 10.0000 chunk 232 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 310 optimal weight: 0.0070 chunk 328 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 294 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- 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 41 ASN I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 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: 0.8018 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27027 Z= 0.165 Angle : 0.476 5.646 36525 Z= 0.245 Chirality : 0.039 0.155 4243 Planarity : 0.003 0.038 4723 Dihedral : 5.360 58.664 3783 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.07 % Allowed : 0.63 % Favored : 99.30 % 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: -0.30 (0.14), residues: 3382 helix: 0.63 (0.13), residues: 1488 sheet: -0.60 (0.22), residues: 500 loop : -0.85 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 95 PHE 0.010 0.001 PHE I 101 TYR 0.018 0.001 TYR F 171 ARG 0.006 0.000 ARG J 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 487 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 485 time to evaluate : 3.185 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 outliers start: 2 outliers final: 0 residues processed: 486 average time/residue: 0.6883 time to fit residues: 537.8555 Evaluate side-chains 390 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8657 ------------------------------------------------------------------------------- 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: 7.9990 chunk 186 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN D 83 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN I 41 ASN J 41 ASN K 41 ASN L 163 GLN M 9 GLN M 41 ASN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27027 Z= 0.339 Angle : 0.603 11.094 36525 Z= 0.307 Chirality : 0.040 0.213 4243 Planarity : 0.003 0.051 4723 Dihedral : 5.617 60.954 3783 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.07 % Allowed : 1.33 % Favored : 98.60 % 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: -0.71 (0.14), residues: 3382 helix: 0.24 (0.13), residues: 1502 sheet: -0.72 (0.23), residues: 460 loop : -1.05 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS N 138 PHE 0.018 0.002 PHE C 245 TYR 0.018 0.002 TYR F 96 ARG 0.004 0.001 ARG K 15 *********************** 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 461 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 459 time to evaluate : 3.178 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 outliers start: 2 outliers final: 2 residues processed: 460 average time/residue: 0.7046 time to fit residues: 528.4204 Evaluate side-chains 364 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 362 time to evaluate : 3.174 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5545 time to fit residues: 5.8568 ------------------------------------------------------------------------------- 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: 6.9990 chunk 295 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 328 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 150 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 GLN ** 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: 0.8131 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27027 Z= 0.331 Angle : 0.582 7.416 36525 Z= 0.304 Chirality : 0.041 0.163 4243 Planarity : 0.003 0.038 4723 Dihedral : 5.794 63.975 3783 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: -0.92 (0.14), residues: 3382 helix: 0.03 (0.13), residues: 1497 sheet: -0.51 (0.21), residues: 528 loop : -1.27 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 73 PHE 0.037 0.002 PHE B 245 TYR 0.019 0.002 TYR E 93 ARG 0.005 0.000 ARG N 22 *********************** 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 437 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 4.015 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 outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.6953 time to fit residues: 490.8247 Evaluate side-chains 355 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 3.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9485 ------------------------------------------------------------------------------- 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: 9.9990 chunk 37 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 276 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 327 optimal weight: 4.9990 chunk 205 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 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: 0.8101 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27027 Z= 0.211 Angle : 0.508 8.678 36525 Z= 0.262 Chirality : 0.040 0.157 4243 Planarity : 0.003 0.038 4723 Dihedral : 5.641 64.608 3783 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.03 % Allowed : 0.70 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3382 helix: 0.40 (0.13), residues: 1496 sheet: -0.32 (0.22), residues: 509 loop : -1.10 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 95 PHE 0.011 0.001 PHE B 245 TYR 0.018 0.001 TYR H 62 ARG 0.004 0.000 ARG K 15 *********************** 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 445 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 3.192 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 outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.7009 time to fit residues: 502.8259 Evaluate side-chains 361 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.164 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9459 ------------------------------------------------------------------------------- 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: 10.0000 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 41 ASN M 41 ASN ** 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: 0.8093 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27027 Z= 0.187 Angle : 0.484 5.868 36525 Z= 0.249 Chirality : 0.039 0.210 4243 Planarity : 0.003 0.034 4723 Dihedral : 5.488 65.294 3783 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3382 helix: 0.63 (0.13), residues: 1497 sheet: -0.24 (0.21), residues: 544 loop : -1.01 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 95 PHE 0.021 0.001 PHE B 245 TYR 0.015 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 452 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 3.209 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 outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.7058 time to fit residues: 514.7359 Evaluate side-chains 365 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 3.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8889 ------------------------------------------------------------------------------- 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: 9.9990 chunk 313 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 305 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 275 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN M 41 ASN ** 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: 0.8093 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27027 Z= 0.179 Angle : 0.487 7.723 36525 Z= 0.249 Chirality : 0.039 0.161 4243 Planarity : 0.003 0.035 4723 Dihedral : 5.409 65.650 3783 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.65 % 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: -0.09 (0.14), residues: 3382 helix: 0.79 (0.13), residues: 1505 sheet: -0.16 (0.23), residues: 497 loop : -0.90 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 230 PHE 0.021 0.001 PHE B 245 TYR 0.015 0.001 TYR F 96 ARG 0.005 0.000 ARG K 15 *********************** 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 450 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 3.206 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 outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.7113 time to fit residues: 522.9663 Evaluate side-chains 364 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9262 ------------------------------------------------------------------------------- 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: 3.9990 chunk 153 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 338 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN M 41 ASN ** 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: 0.8138 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 27027 Z= 0.308 Angle : 0.560 8.968 36525 Z= 0.290 Chirality : 0.040 0.191 4243 Planarity : 0.003 0.032 4723 Dihedral : 5.600 65.945 3783 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: -0.50 (0.14), residues: 3382 helix: 0.45 (0.13), residues: 1509 sheet: -0.34 (0.22), residues: 510 loop : -1.14 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 73 PHE 0.022 0.001 PHE B 245 TYR 0.017 0.001 TYR F 96 ARG 0.006 0.001 ARG N 22 ********************** 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 437 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 436 time to evaluate : 3.151 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 outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.7405 time to fit residues: 531.7644 Evaluate side-chains 347 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9827 ------------------------------------------------------------------------------- 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: 4.9990 chunk 82 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN C 230 HIS F 342 ASN H 81 GLN I 41 ASN I 150 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN L 41 ASN M 41 ASN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065484 restraints weight = 257209.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068850 restraints weight = 118685.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071085 restraints weight = 71631.037| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27027 Z= 0.194 Angle : 0.488 5.959 36525 Z= 0.252 Chirality : 0.040 0.206 4243 Planarity : 0.003 0.034 4723 Dihedral : 5.519 67.759 3783 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.79 % 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: -0.18 (0.14), residues: 3382 helix: 0.72 (0.13), residues: 1500 sheet: -0.24 (0.22), residues: 510 loop : -0.93 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 230 PHE 0.020 0.001 PHE B 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: 9973.11 seconds wall clock time: 174 minutes 2.11 seconds (10442.11 seconds total)