Starting phenix.real_space_refine on Thu Dec 7 16:13:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po3_20408/12_2023/6po3_20408_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po3_20408/12_2023/6po3_20408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po3_20408/12_2023/6po3_20408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po3_20408/12_2023/6po3_20408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po3_20408/12_2023/6po3_20408_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po3_20408/12_2023/6po3_20408_trim_updated.pdb" } resolution = 4.28 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 16679 2.51 5 N 4518 2.21 5 O 5168 1.98 5 H 26724 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 392": "OD1" <-> "OD2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 103": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 382": "OD1" <-> "OD2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F ASP 294": "OD1" <-> "OD2" Residue "F PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 392": "OD1" <-> "OD2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 37": "OD1" <-> "OD2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I ASP 86": "OD1" <-> "OD2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 "I PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 8": "OE1" <-> "OE2" 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 PHE 30": "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 "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 30": "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 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 "L ASP 171": "OD1" <-> "OD2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 60": "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 "M GLU 181": "OE1" <-> "OE2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 60": "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 ASP 167": "OD1" <-> "OD2" 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: 53225 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5330 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 2 Chain: "B" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "D" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5380 Classifications: {'peptide': 349} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "E" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5336 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5125 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 3 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" 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: "J" 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: "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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" 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: "N" 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: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.59, per 1000 atoms: 0.33 Number of scatterers: 53225 At special positions: 0 Unit cell: (147.32, 141.52, 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 5168 8.00 N 4518 7.00 C 16679 6.00 H 26724 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=0, symmetry=0 Time building additional restraints: 30.55 Conformation dependent library (CDL) restraints added in 4.2 seconds 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 36 sheets defined 44.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.812A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.586A pdb=" N LYS A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.549A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.671A pdb=" N LYS A 164 " --> pdb=" O ILE A 161 " (cutoff:3.500A) 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 186 through 189 Processing helix chain 'A' and resid 205 through 216 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 261 Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.710A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 369 through 379 removed outlier: 4.172A pdb=" N ARG A 373 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.719A 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: 3.810A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 98 removed outlier: 3.886A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.569A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.528A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 168 " --> pdb=" O LEU B 165 " (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 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.572A pdb=" N LEU B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.655A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.612A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.903A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 removed outlier: 3.728A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.502A pdb=" N ALA B 378 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.675A 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: 3.685A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.502A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.705A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.797A 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: 4.477A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.597A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 292 through 298 removed outlier: 3.771A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.823A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.530A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 removed outlier: 4.006A pdb=" N GLU C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 365 removed outlier: 3.834A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 387 removed outlier: 3.505A pdb=" N GLU C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 378 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 383 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET C 384 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 387 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.602A 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 76 Processing helix chain 'D' and resid 82 through 100 removed outlier: 3.983A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.820A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.960A 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 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.490A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.521A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.951A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.651A 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 327 removed outlier: 3.704A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.623A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 365 removed outlier: 3.504A pdb=" N ASP D 356 " --> pdb=" O ASP D 352 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 387 removed outlier: 3.764A pdb=" N GLU D 377 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 378 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP D 382 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 385 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 387 " --> pdb=" O MET D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.659A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'E' and resid 67 through 77 removed outlier: 3.637A pdb=" N HIS E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 101 Processing helix chain 'E' and resid 125 through 136 removed outlier: 3.550A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.581A pdb=" N LYS E 164 " --> pdb=" O ILE E 161 " (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 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.454A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 263 Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.758A pdb=" N LEU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 283 through 289' Processing helix chain 'E' and resid 292 through 298 removed outlier: 3.710A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 321 through 327 Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.982A pdb=" N ARG E 373 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 378 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.792A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 101 removed outlier: 3.630A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 136 removed outlier: 3.743A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.656A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 4.507A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (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: 3.642A 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: 3.583A pdb=" N ILE F 296 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 3.871A 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 327 removed outlier: 3.632A pdb=" N ILE F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 Processing helix chain 'F' and resid 352 through 365 removed outlier: 3.530A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 387 removed outlier: 3.681A pdb=" N VAL F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.837A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.723A pdb=" N ALA H 45 " --> pdb=" O ASN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.744A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 4.191A 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 168 Processing helix chain 'H' and resid 176 through 181 removed outlier: 3.573A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.795A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 removed outlier: 3.715A pdb=" N ALA I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.762A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 4.215A 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: 3.656A pdb=" N VAL I 180 " --> pdb=" O ALA I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.910A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 removed outlier: 3.658A pdb=" N ALA J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.831A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.169A 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 Processing helix chain 'J' and resid 161 through 167 Processing helix chain 'J' and resid 176 through 181 removed outlier: 3.637A pdb=" N VAL J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.917A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 removed outlier: 3.574A pdb=" N ALA K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.700A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.144A 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 168 Processing helix chain 'K' and resid 176 through 181 removed outlier: 3.556A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.847A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.662A pdb=" N ALA L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.612A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 4.180A 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: 3.689A pdb=" N VAL L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.869A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.685A pdb=" N ALA M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.776A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 4.201A 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 removed outlier: 3.524A pdb=" N ILE M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 167 Processing helix chain 'M' and resid 176 through 181 removed outlier: 3.770A pdb=" N VAL M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 176 through 181' Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.939A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 Processing helix chain 'N' and resid 70 through 82 removed outlier: 3.774A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 4.142A 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: 3.665A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 311 through 313 removed outlier: 6.899A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.744A pdb=" N ALA A 220 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 238 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.549A pdb=" N VAL A 397 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 410 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.955A pdb=" N ILE B 180 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 244 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE B 183 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.353A 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 219 through 223 removed outlier: 4.066A pdb=" N ALA B 220 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.534A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 312 through 314 Processing sheet with id= H, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.616A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 180 through 184 removed outlier: 6.388A pdb=" N LEU D 244 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE D 183 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE D 246 " --> pdb=" O ILE D 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.519A pdb=" N ILE D 398 " --> pdb=" O GLU D 349 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 312 through 314 removed outlier: 3.502A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 219 through 222 removed outlier: 4.036A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.521A pdb=" N GLU E 349 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.484A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.930A 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 347 through 350 removed outlier: 3.697A pdb=" N ILE F 398 " --> pdb=" O GLU F 349 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 5 through 8 Processing sheet with id= Q, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.690A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= S, first strand: chain 'I' and resid 5 through 8 Processing sheet with id= T, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.647A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 119 through 121 Processing sheet with id= V, first strand: chain 'J' and resid 5 through 8 Processing sheet with id= W, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.739A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 119 through 121 removed outlier: 3.547A pdb=" N ILE J 121 " --> pdb=" O ARG J 172 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 5 through 8 Processing sheet with id= Z, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.706A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AB, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= AC, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.493A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 119 through 121 Processing sheet with id= AE, first strand: chain 'M' and resid 5 through 8 removed outlier: 3.596A pdb=" N GLU M 8 " --> pdb=" O ARG M 15 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG M 15 " --> pdb=" O GLU M 8 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.593A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS M 91 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AH, first strand: chain 'N' and resid 5 through 8 removed outlier: 3.716A pdb=" N ARG N 15 " --> pdb=" O GLU N 8 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.717A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 119 through 121 940 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.27 Time building geometry restraints manager: 32.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 26704 1.06 - 1.28: 4663 1.28 - 1.50: 10494 1.50 - 1.73: 11524 1.73 - 1.95: 213 Bond restraints: 53598 Sorted by residual: bond pdb=" C ILE D 301 " pdb=" N PRO D 302 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.48e+00 bond pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.91e+00 bond pdb=" N LEU F 64 " pdb=" CA LEU F 64 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.73e+00 bond pdb=" C PRO D 223 " pdb=" N PRO D 224 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 3.13e+00 bond pdb=" N LEU I 2 " pdb=" CA LEU I 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 53593 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.54: 3579 107.54 - 114.69: 66288 114.69 - 121.85: 18034 121.85 - 129.00: 9221 129.00 - 136.16: 148 Bond angle restraints: 97270 Sorted by residual: angle pdb=" CA GLY F 206 " pdb=" C GLY F 206 " pdb=" N VAL F 207 " ideal model delta sigma weight residual 116.81 111.29 5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" C ASN C 101 " pdb=" N GLY C 102 " pdb=" CA GLY C 102 " ideal model delta sigma weight residual 121.41 132.08 -10.67 1.96e+00 2.60e-01 2.96e+01 angle pdb=" N SER C 105 " pdb=" CA SER C 105 " pdb=" C SER C 105 " ideal model delta sigma weight residual 109.59 101.93 7.66 1.61e+00 3.86e-01 2.27e+01 angle pdb=" C GLY F 204 " pdb=" N GLU F 205 " pdb=" CA GLU F 205 " ideal model delta sigma weight residual 121.54 129.10 -7.56 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C GLU F 205 " pdb=" N GLY F 206 " pdb=" CA GLY F 206 " ideal model delta sigma weight residual 119.94 124.18 -4.24 1.11e+00 8.12e-01 1.46e+01 ... (remaining 97265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 22181 17.31 - 34.63: 1589 34.63 - 51.94: 280 51.94 - 69.26: 33 69.26 - 86.57: 14 Dihedral angle restraints: 24097 sinusoidal: 13263 harmonic: 10834 Sorted by residual: dihedral pdb=" CA LYS C 366 " pdb=" CB LYS C 366 " pdb=" CG LYS C 366 " pdb=" CD LYS C 366 " ideal model delta sinusoidal sigma weight residual -60.00 -119.15 59.15 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " pdb=" OD1 ASP A 194 " ideal model delta sinusoidal sigma weight residual -30.00 -82.16 52.16 1 2.00e+01 2.50e-03 9.28e+00 dihedral pdb=" N ARG E 370 " pdb=" CA ARG E 370 " pdb=" CB ARG E 370 " pdb=" CG ARG E 370 " ideal model delta sinusoidal sigma weight residual -180.00 -129.28 -50.72 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 24094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3199 0.042 - 0.084: 739 0.084 - 0.126: 249 0.126 - 0.168: 41 0.168 - 0.210: 1 Chirality restraints: 4229 Sorted by residual: chirality pdb=" CA ASP C 103 " pdb=" N ASP C 103 " pdb=" C ASP C 103 " pdb=" CB ASP C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA SER C 105 " pdb=" N SER C 105 " pdb=" C SER C 105 " pdb=" CB SER C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 4226 not shown) Planarity restraints: 7953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 370 " 0.089 9.50e-02 1.11e+02 9.26e-02 1.74e+02 pdb=" NE ARG B 370 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 370 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 370 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 370 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 370 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 370 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG B 370 " -0.172 2.00e-02 2.50e+03 pdb="HH22 ARG B 370 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 195 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO E 196 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 176 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO K 177 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO K 177 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 177 " 0.031 5.00e-02 4.00e+02 ... (remaining 7950 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 319 2.01 - 2.65: 74805 2.65 - 3.30: 152312 3.30 - 3.95: 191368 3.95 - 4.60: 300653 Nonbonded interactions: 719457 Sorted by model distance: nonbonded pdb=" OD1 ASP C 399 " pdb=" HG SER C 401 " model vdw 1.357 1.850 nonbonded pdb=" HZ2 LYS C 112 " pdb=" O SER C 241 " model vdw 1.397 1.850 nonbonded pdb=" OD1 ASP E 144 " pdb=" HG1 THR E 146 " model vdw 1.425 1.850 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.429 1.850 nonbonded pdb=" O LEU C 326 " pdb=" HG1 THR C 334 " model vdw 1.434 1.850 ... (remaining 719452 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 64 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 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'B' and (resid 64 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 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'C' and (resid 64 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 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'D' and (resid 64 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 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'E' and (resid 64 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 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'F' and (resid 64 through 225 or resid 233 through 259 or (resid 260 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 NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 261 through 413)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 0.560 Extract box with map and model: 3.620 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 121.480 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.190 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:2.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 0.054 26874 Z= 0.222 Angle : 0.652 10.669 36325 Z= 0.359 Chirality : 0.042 0.210 4229 Planarity : 0.004 0.076 4695 Dihedral : 11.393 81.904 10214 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 3361 helix: -1.01 (0.11), residues: 1456 sheet: -0.55 (0.24), residues: 426 loop : -1.24 (0.14), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 95 PHE 0.014 0.001 PHE A 270 TYR 0.009 0.001 TYR E 93 ARG 0.013 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 913 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 913 time to evaluate : 3.152 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 outliers start: 0 outliers final: 0 residues processed: 913 average time/residue: 0.8346 time to fit residues: 1126.0491 Evaluate side-chains 489 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 141 optimal weight: 0.0870 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 overall best weight: 2.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 114 ASN A 195 ASN A 225 GLN B 68 HIS B 185 GLN B 225 GLN D 167 GLN E 83 GLN ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN F 331 ASN F 336 GLN H 41 ASN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 HIS J 156 HIS J 163 GLN K 41 ASN K 116 ASN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 116 ASN N 41 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26874 Z= 0.203 Angle : 0.545 5.580 36325 Z= 0.293 Chirality : 0.041 0.166 4229 Planarity : 0.004 0.066 4695 Dihedral : 6.178 59.111 3757 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -0.23 (0.14), residues: 3361 helix: 0.76 (0.13), residues: 1471 sheet: -0.16 (0.21), residues: 527 loop : -1.10 (0.15), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 68 PHE 0.018 0.002 PHE D 298 TYR 0.016 0.001 TYR E 93 ARG 0.009 0.001 ARG K 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 587 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 3.870 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 outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.7837 time to fit residues: 712.0826 Evaluate side-chains 423 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 3.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 330 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS E 167 GLN E 338 GLN F 68 HIS F 106 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN L 41 ASN L 116 ASN M 150 ASN N 129 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 26874 Z= 0.315 Angle : 0.584 8.151 36325 Z= 0.307 Chirality : 0.042 0.249 4229 Planarity : 0.004 0.062 4695 Dihedral : 6.296 68.945 3757 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.30 (0.14), residues: 3361 helix: 0.67 (0.13), residues: 1526 sheet: -0.08 (0.21), residues: 537 loop : -1.24 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 95 PHE 0.019 0.001 PHE E 298 TYR 0.022 0.002 TYR K 62 ARG 0.024 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 3.132 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 outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.7409 time to fit residues: 602.5494 Evaluate side-chains 402 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 3.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 205 optimal weight: 0.0470 chunk 306 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 290 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN F 106 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN J 163 GLN K 9 GLN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 HIS L 41 ASN L 116 ASN L 156 HIS ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26874 Z= 0.181 Angle : 0.483 5.520 36325 Z= 0.250 Chirality : 0.040 0.144 4229 Planarity : 0.003 0.038 4695 Dihedral : 5.820 71.543 3757 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3361 helix: 0.91 (0.13), residues: 1503 sheet: 0.00 (0.22), residues: 525 loop : -1.14 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS I 138 PHE 0.023 0.001 PHE L 173 TYR 0.020 0.001 TYR K 62 ARG 0.012 0.000 ARG F 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 3.103 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: 510 average time/residue: 0.7368 time to fit residues: 584.9955 Evaluate side-chains 398 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 3.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN I 129 GLN J 41 ASN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 116 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 26874 Z= 0.389 Angle : 0.634 8.085 36325 Z= 0.334 Chirality : 0.042 0.163 4229 Planarity : 0.004 0.046 4695 Dihedral : 6.131 84.331 3757 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3361 helix: 0.45 (0.13), residues: 1523 sheet: -0.25 (0.21), residues: 527 loop : -1.55 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.001 HIS A 68 PHE 0.019 0.002 PHE D 298 TYR 0.023 0.002 TYR K 128 ARG 0.014 0.001 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 470 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 3.152 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 outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.7929 time to fit residues: 581.2499 Evaluate side-chains 371 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 0.0070 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN J 41 ASN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 116 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26874 Z= 0.225 Angle : 0.506 5.428 36325 Z= 0.265 Chirality : 0.040 0.153 4229 Planarity : 0.003 0.045 4695 Dihedral : 5.899 82.804 3757 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3361 helix: 0.72 (0.13), residues: 1514 sheet: -0.14 (0.22), residues: 509 loop : -1.38 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 95 PHE 0.016 0.001 PHE D 298 TYR 0.012 0.001 TYR K 62 ARG 0.005 0.000 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 3.273 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 outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.7465 time to fit residues: 546.5485 Evaluate side-chains 365 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 3.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 41 ASN J 41 ASN K 129 GLN K 193 ASN L 41 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26874 Z= 0.196 Angle : 0.486 5.658 36325 Z= 0.251 Chirality : 0.040 0.166 4229 Planarity : 0.003 0.071 4695 Dihedral : 5.731 78.373 3757 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3361 helix: 0.91 (0.13), residues: 1518 sheet: -0.12 (0.22), residues: 509 loop : -1.27 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 95 PHE 0.013 0.001 PHE F 270 TYR 0.017 0.001 TYR K 128 ARG 0.008 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.7591 time to fit residues: 552.2461 Evaluate side-chains 364 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.164 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 41 ASN I 41 ASN J 41 ASN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 116 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26874 Z= 0.200 Angle : 0.488 5.624 36325 Z= 0.253 Chirality : 0.040 0.164 4229 Planarity : 0.003 0.072 4695 Dihedral : 5.676 75.807 3757 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % 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: -0.12 (0.14), residues: 3361 helix: 0.95 (0.13), residues: 1522 sheet: -0.15 (0.22), residues: 509 loop : -1.23 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 95 PHE 0.016 0.001 PHE L 173 TYR 0.017 0.001 TYR M 128 ARG 0.012 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 3.137 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 outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.7747 time to fit residues: 554.3377 Evaluate side-chains 366 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 3.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 285 optimal weight: 8.9990 chunk 300 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: C 101 ASN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 41 ASN I 41 ASN J 41 ASN J 156 HIS K 81 GLN L 41 ASN L 116 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26874 Z= 0.257 Angle : 0.522 6.437 36325 Z= 0.271 Chirality : 0.040 0.280 4229 Planarity : 0.003 0.071 4695 Dihedral : 5.787 73.837 3757 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3361 helix: 0.82 (0.13), residues: 1524 sheet: -0.23 (0.23), residues: 467 loop : -1.26 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 95 PHE 0.024 0.002 PHE L 173 TYR 0.016 0.001 TYR M 77 ARG 0.009 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 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 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 3.145 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 outliers start: 1 outliers final: 1 residues processed: 445 average time/residue: 0.7751 time to fit residues: 545.0084 Evaluate side-chains 365 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 3.236 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4947 time to fit residues: 4.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 151 optimal weight: 0.1980 chunk 221 optimal weight: 0.6980 chunk 334 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 41 ASN J 41 ASN L 41 ASN L 116 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26874 Z= 0.191 Angle : 0.486 6.140 36325 Z= 0.252 Chirality : 0.040 0.152 4229 Planarity : 0.003 0.072 4695 Dihedral : 5.733 74.393 3757 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % 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: -0.09 (0.14), residues: 3361 helix: 0.99 (0.14), residues: 1516 sheet: -0.17 (0.24), residues: 467 loop : -1.19 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 95 PHE 0.034 0.001 PHE L 173 TYR 0.023 0.001 TYR M 77 ARG 0.012 0.000 ARG F 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6722 Ramachandran restraints generated. 3361 Oldfield, 0 Emsley, 3361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 3.171 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 outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.7418 time to fit residues: 521.1331 Evaluate side-chains 370 residues out of total 2850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 3.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN H 41 ASN I 150 ASN J 41 ASN L 41 ASN L 116 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.103167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084485 restraints weight = 214506.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087005 restraints weight = 127771.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088712 restraints weight = 90011.136| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26874 Z= 0.330 Angle : 0.571 7.118 36325 Z= 0.299 Chirality : 0.041 0.184 4229 Planarity : 0.004 0.069 4695 Dihedral : 5.990 72.984 3757 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.04 % Allowed : 0.11 % Favored : 99.86 % 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: -0.53 (0.14), residues: 3361 helix: 0.66 (0.13), residues: 1529 sheet: -0.50 (0.22), residues: 492 loop : -1.44 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 95 PHE 0.019 0.002 PHE J 101 TYR 0.016 0.002 TYR K 128 ARG 0.009 0.001 ARG I 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10293.12 seconds wall clock time: 178 minutes 49.57 seconds (10729.57 seconds total)