Starting phenix.real_space_refine (version: dev) on Mon May 16 08:16:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t63_10383/05_2022/6t63_10383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t63_10383/05_2022/6t63_10383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t63_10383/05_2022/6t63_10383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t63_10383/05_2022/6t63_10383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t63_10383/05_2022/6t63_10383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t63_10383/05_2022/6t63_10383.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.195 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F ASP 203": "OD1" <-> "OD2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F ASP 290": "OD1" <-> "OD2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F GLU 337": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 182": "OD1" <-> "OD2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H ASP 196": "OD1" <-> "OD2" Residue "H ASP 247": "OD1" <-> "OD2" Residue "H GLU 287": "OE1" <-> "OE2" Residue "H PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 290": "OD1" <-> "OD2" Residue "H ASP 311": "OD1" <-> "OD2" Residue "H GLU 336": "OE1" <-> "OE2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ASP 196": "OD1" <-> "OD2" Residue "I ASP 247": "OD1" <-> "OD2" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 290": "OD1" <-> "OD2" Residue "I ASP 311": "OD1" <-> "OD2" Residue "I GLU 336": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E ASP 203": "OD1" <-> "OD2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "G PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 247": "OD1" <-> "OD2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G ASP 290": "OD1" <-> "OD2" Residue "G ASP 333": "OD1" <-> "OD2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "J GLU 176": "OE1" <-> "OE2" Residue "J ASP 182": "OD1" <-> "OD2" Residue "J ASP 196": "OD1" <-> "OD2" Residue "J ASP 203": "OD1" <-> "OD2" Residue "J PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 247": "OD1" <-> "OD2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "J GLU 321": "OE1" <-> "OE2" Residue "J GLU 332": "OE1" <-> "OE2" Residue "J ASP 333": "OD1" <-> "OD2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K ASP 196": "OD1" <-> "OD2" Residue "K ASP 203": "OD1" <-> "OD2" Residue "K PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 247": "OD1" <-> "OD2" Residue "K GLU 259": "OE1" <-> "OE2" Residue "K ASP 290": "OD1" <-> "OD2" Residue "K ASP 333": "OD1" <-> "OD2" Residue "K GLU 337": "OE1" <-> "OE2" Residue "L GLU 176": "OE1" <-> "OE2" Residue "L ASP 196": "OD1" <-> "OD2" Residue "L ASP 247": "OD1" <-> "OD2" Residue "L GLU 287": "OE1" <-> "OE2" Residue "L PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 290": "OD1" <-> "OD2" Residue "L ASP 311": "OD1" <-> "OD2" Residue "L GLU 336": "OE1" <-> "OE2" Residue "O ASP 196": "OD1" <-> "OD2" Residue "O ASP 203": "OD1" <-> "OD2" Residue "O PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 247": "OD1" <-> "OD2" Residue "O GLU 259": "OE1" <-> "OE2" Residue "O ASP 290": "OD1" <-> "OD2" Residue "O ASP 333": "OD1" <-> "OD2" Residue "O GLU 337": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M GLU 176": "OE1" <-> "OE2" Residue "M ASP 182": "OD1" <-> "OD2" Residue "M ASP 196": "OD1" <-> "OD2" Residue "M ASP 203": "OD1" <-> "OD2" Residue "M PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 247": "OD1" <-> "OD2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "M GLU 321": "OE1" <-> "OE2" Residue "M GLU 332": "OE1" <-> "OE2" Residue "M ASP 333": "OD1" <-> "OD2" Residue "M GLU 336": "OE1" <-> "OE2" Residue "Q GLU 176": "OE1" <-> "OE2" Residue "Q ASP 196": "OD1" <-> "OD2" Residue "Q ASP 247": "OD1" <-> "OD2" Residue "Q GLU 287": "OE1" <-> "OE2" Residue "Q PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 290": "OD1" <-> "OD2" Residue "Q ASP 311": "OD1" <-> "OD2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "R GLU 176": "OE1" <-> "OE2" Residue "R ASP 196": "OD1" <-> "OD2" Residue "R ASP 247": "OD1" <-> "OD2" Residue "R GLU 287": "OE1" <-> "OE2" Residue "R PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 290": "OD1" <-> "OD2" Residue "R ASP 311": "OD1" <-> "OD2" Residue "R GLU 336": "OE1" <-> "OE2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "N GLU 176": "OE1" <-> "OE2" Residue "N ASP 182": "OD1" <-> "OD2" Residue "N ASP 196": "OD1" <-> "OD2" Residue "N ASP 203": "OD1" <-> "OD2" Residue "N PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 247": "OD1" <-> "OD2" Residue "N GLU 320": "OE1" <-> "OE2" Residue "N GLU 321": "OE1" <-> "OE2" Residue "N GLU 332": "OE1" <-> "OE2" Residue "N ASP 333": "OD1" <-> "OD2" Residue "N GLU 336": "OE1" <-> "OE2" Residue "P ASP 196": "OD1" <-> "OD2" Residue "P ASP 203": "OD1" <-> "OD2" Residue "P PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 247": "OD1" <-> "OD2" Residue "P GLU 259": "OE1" <-> "OE2" Residue "P ASP 290": "OD1" <-> "OD2" Residue "P ASP 333": "OD1" <-> "OD2" Residue "P GLU 337": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 30978 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "B" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "H" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "I" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "J" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "K" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "L" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "O" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "M" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "Q" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "R" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "N" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "P" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Time building chain proxies: 16.52, per 1000 atoms: 0.53 Number of scatterers: 30978 At special positions: 0 Unit cell: (169.683, 163.437, 118.674, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 5832 8.00 N 5472 7.00 C 19458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 342 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 342 " distance=2.04 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 342 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 342 " distance=2.03 Simple disulfide: pdb=" SG CYS H 322 " - pdb=" SG CYS H 342 " distance=2.04 Simple disulfide: pdb=" SG CYS I 322 " - pdb=" SG CYS I 342 " distance=2.04 Simple disulfide: pdb=" SG CYS E 322 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 322 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS J 322 " - pdb=" SG CYS J 342 " distance=2.03 Simple disulfide: pdb=" SG CYS K 322 " - pdb=" SG CYS K 342 " distance=2.03 Simple disulfide: pdb=" SG CYS L 322 " - pdb=" SG CYS L 342 " distance=2.04 Simple disulfide: pdb=" SG CYS O 322 " - pdb=" SG CYS O 342 " distance=2.03 Simple disulfide: pdb=" SG CYS M 322 " - pdb=" SG CYS M 342 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 322 " - pdb=" SG CYS Q 342 " distance=2.04 Simple disulfide: pdb=" SG CYS R 322 " - pdb=" SG CYS R 342 " distance=2.04 Simple disulfide: pdb=" SG CYS N 322 " - pdb=" SG CYS N 342 " distance=2.03 Simple disulfide: pdb=" SG CYS P 322 " - pdb=" SG CYS P 342 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.95 Conformation dependent library (CDL) restraints added in 4.4 seconds 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7344 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 0 sheets defined 67.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.532A pdb=" N VAL A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 189 through 209 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.657A pdb=" N MET A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'A' and resid 284 through 300 removed outlier: 3.576A pdb=" N PHE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 5.198A pdb=" N ILE A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.733A pdb=" N THR B 153 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 190 through 209 Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.578A pdb=" N ARG B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 269 removed outlier: 3.632A pdb=" N ILE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 300 removed outlier: 3.888A pdb=" N GLY B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'C' and resid 144 through 154 removed outlier: 3.581A pdb=" N THR C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 190 through 209 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 246 through 268 Processing helix chain 'C' and resid 284 through 300 removed outlier: 3.652A pdb=" N PHE C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 removed outlier: 4.739A pdb=" N ILE C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 334 through 342 removed outlier: 3.504A pdb=" N CYS C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 Processing helix chain 'F' and resid 144 through 155 removed outlier: 3.732A pdb=" N THR F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 Processing helix chain 'F' and resid 173 through 182 Processing helix chain 'F' and resid 190 through 209 Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.576A pdb=" N ARG F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 269 removed outlier: 3.632A pdb=" N ILE F 269 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 300 removed outlier: 3.888A pdb=" N GLY F 300 " --> pdb=" O ILE F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'F' and resid 334 through 342 Processing helix chain 'F' and resid 347 through 358 Processing helix chain 'D' and resid 144 through 154 removed outlier: 3.532A pdb=" N VAL D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 189 through 209 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.657A pdb=" N MET D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 268 Processing helix chain 'D' and resid 284 through 300 removed outlier: 3.575A pdb=" N PHE D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 317 removed outlier: 5.198A pdb=" N ILE D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 347 through 358 Processing helix chain 'H' and resid 144 through 154 removed outlier: 3.581A pdb=" N THR H 153 " --> pdb=" O ASN H 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN H 154 " --> pdb=" O THR H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 169 Processing helix chain 'H' and resid 173 through 183 Processing helix chain 'H' and resid 190 through 209 Processing helix chain 'H' and resid 227 through 232 Processing helix chain 'H' and resid 246 through 268 Processing helix chain 'H' and resid 284 through 300 removed outlier: 3.652A pdb=" N PHE H 288 " --> pdb=" O PRO H 284 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY H 300 " --> pdb=" O ILE H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 317 removed outlier: 4.739A pdb=" N ILE H 315 " --> pdb=" O ASP H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 326 Processing helix chain 'H' and resid 334 through 342 removed outlier: 3.503A pdb=" N CYS H 342 " --> pdb=" O LYS H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 357 Processing helix chain 'I' and resid 144 through 154 removed outlier: 3.583A pdb=" N THR I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN I 154 " --> pdb=" O THR I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 169 Processing helix chain 'I' and resid 173 through 183 Processing helix chain 'I' and resid 190 through 209 Processing helix chain 'I' and resid 227 through 232 Processing helix chain 'I' and resid 246 through 268 Processing helix chain 'I' and resid 284 through 300 removed outlier: 3.652A pdb=" N PHE I 288 " --> pdb=" O PRO I 284 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY I 300 " --> pdb=" O ILE I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 317 removed outlier: 4.740A pdb=" N ILE I 315 " --> pdb=" O ASP I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 334 through 342 removed outlier: 3.504A pdb=" N CYS I 342 " --> pdb=" O LYS I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 357 Processing helix chain 'E' and resid 144 through 154 removed outlier: 3.533A pdb=" N VAL E 148 " --> pdb=" O TYR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 173 through 182 Processing helix chain 'E' and resid 189 through 209 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.658A pdb=" N MET E 242 " --> pdb=" O ARG E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 268 Processing helix chain 'E' and resid 284 through 300 removed outlier: 3.574A pdb=" N PHE E 288 " --> pdb=" O PRO E 284 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY E 300 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 317 removed outlier: 5.198A pdb=" N ILE E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'E' and resid 347 through 358 Processing helix chain 'G' and resid 144 through 155 removed outlier: 3.732A pdb=" N THR G 153 " --> pdb=" O ASN G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 169 Processing helix chain 'G' and resid 173 through 182 Processing helix chain 'G' and resid 190 through 209 Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.575A pdb=" N ARG G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 269 removed outlier: 3.632A pdb=" N ILE G 269 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 300 removed outlier: 3.888A pdb=" N GLY G 300 " --> pdb=" O ILE G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 314 Processing helix chain 'G' and resid 320 through 325 Processing helix chain 'G' and resid 334 through 342 Processing helix chain 'G' and resid 347 through 358 Processing helix chain 'J' and resid 144 through 154 removed outlier: 3.531A pdb=" N VAL J 148 " --> pdb=" O TYR J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 169 Processing helix chain 'J' and resid 173 through 182 Processing helix chain 'J' and resid 189 through 209 Processing helix chain 'J' and resid 227 through 233 Processing helix chain 'J' and resid 237 through 242 removed outlier: 3.657A pdb=" N MET J 242 " --> pdb=" O ARG J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 268 Processing helix chain 'J' and resid 284 through 300 removed outlier: 3.576A pdb=" N PHE J 288 " --> pdb=" O PRO J 284 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY J 300 " --> pdb=" O ILE J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 317 removed outlier: 5.197A pdb=" N ILE J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 326 Processing helix chain 'J' and resid 334 through 342 Processing helix chain 'J' and resid 347 through 358 Processing helix chain 'K' and resid 144 through 155 removed outlier: 3.733A pdb=" N THR K 153 " --> pdb=" O ASN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 169 Processing helix chain 'K' and resid 173 through 182 Processing helix chain 'K' and resid 190 through 209 Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.575A pdb=" N ARG K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 269 removed outlier: 3.631A pdb=" N ILE K 269 " --> pdb=" O ILE K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 300 removed outlier: 3.887A pdb=" N GLY K 300 " --> pdb=" O ILE K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 314 Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'K' and resid 334 through 342 Processing helix chain 'K' and resid 347 through 358 Processing helix chain 'L' and resid 144 through 154 removed outlier: 3.581A pdb=" N THR L 153 " --> pdb=" O ASN L 149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN L 154 " --> pdb=" O THR L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 169 Processing helix chain 'L' and resid 173 through 183 Processing helix chain 'L' and resid 190 through 209 Processing helix chain 'L' and resid 227 through 232 Processing helix chain 'L' and resid 246 through 268 Processing helix chain 'L' and resid 284 through 300 removed outlier: 3.650A pdb=" N PHE L 288 " --> pdb=" O PRO L 284 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY L 300 " --> pdb=" O ILE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 317 removed outlier: 4.739A pdb=" N ILE L 315 " --> pdb=" O ASP L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 326 Processing helix chain 'L' and resid 334 through 342 removed outlier: 3.504A pdb=" N CYS L 342 " --> pdb=" O LYS L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 347 through 357 Processing helix chain 'O' and resid 144 through 155 removed outlier: 3.733A pdb=" N THR O 153 " --> pdb=" O ASN O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 169 Processing helix chain 'O' and resid 173 through 182 Processing helix chain 'O' and resid 190 through 209 Processing helix chain 'O' and resid 227 through 232 removed outlier: 3.576A pdb=" N ARG O 232 " --> pdb=" O ALA O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 246 through 269 removed outlier: 3.630A pdb=" N ILE O 269 " --> pdb=" O ILE O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 300 removed outlier: 3.888A pdb=" N GLY O 300 " --> pdb=" O ILE O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 320 through 325 Processing helix chain 'O' and resid 334 through 342 Processing helix chain 'O' and resid 347 through 358 Processing helix chain 'M' and resid 144 through 154 removed outlier: 3.532A pdb=" N VAL M 148 " --> pdb=" O TYR M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 169 Processing helix chain 'M' and resid 173 through 182 Processing helix chain 'M' and resid 189 through 209 Processing helix chain 'M' and resid 227 through 233 Processing helix chain 'M' and resid 237 through 242 removed outlier: 3.657A pdb=" N MET M 242 " --> pdb=" O ARG M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 268 Processing helix chain 'M' and resid 284 through 300 removed outlier: 3.575A pdb=" N PHE M 288 " --> pdb=" O PRO M 284 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY M 300 " --> pdb=" O ILE M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 317 removed outlier: 5.198A pdb=" N ILE M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 326 Processing helix chain 'M' and resid 334 through 342 Processing helix chain 'M' and resid 347 through 358 Processing helix chain 'Q' and resid 144 through 154 removed outlier: 3.581A pdb=" N THR Q 153 " --> pdb=" O ASN Q 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN Q 154 " --> pdb=" O THR Q 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 169 Processing helix chain 'Q' and resid 173 through 183 Processing helix chain 'Q' and resid 190 through 209 Processing helix chain 'Q' and resid 227 through 232 Processing helix chain 'Q' and resid 246 through 268 Processing helix chain 'Q' and resid 284 through 300 removed outlier: 3.653A pdb=" N PHE Q 288 " --> pdb=" O PRO Q 284 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY Q 300 " --> pdb=" O ILE Q 296 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 317 removed outlier: 4.739A pdb=" N ILE Q 315 " --> pdb=" O ASP Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 319 through 326 Processing helix chain 'Q' and resid 334 through 342 removed outlier: 3.503A pdb=" N CYS Q 342 " --> pdb=" O LYS Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'R' and resid 144 through 154 removed outlier: 3.581A pdb=" N THR R 153 " --> pdb=" O ASN R 149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN R 154 " --> pdb=" O THR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 169 Processing helix chain 'R' and resid 173 through 183 Processing helix chain 'R' and resid 190 through 209 Processing helix chain 'R' and resid 227 through 232 Processing helix chain 'R' and resid 246 through 268 Processing helix chain 'R' and resid 284 through 300 removed outlier: 3.652A pdb=" N PHE R 288 " --> pdb=" O PRO R 284 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 317 removed outlier: 4.740A pdb=" N ILE R 315 " --> pdb=" O ASP R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 326 Processing helix chain 'R' and resid 334 through 342 removed outlier: 3.503A pdb=" N CYS R 342 " --> pdb=" O LYS R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'N' and resid 144 through 154 removed outlier: 3.533A pdb=" N VAL N 148 " --> pdb=" O TYR N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 169 Processing helix chain 'N' and resid 173 through 182 Processing helix chain 'N' and resid 189 through 209 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 237 through 242 removed outlier: 3.658A pdb=" N MET N 242 " --> pdb=" O ARG N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 246 through 268 Processing helix chain 'N' and resid 284 through 300 removed outlier: 3.575A pdb=" N PHE N 288 " --> pdb=" O PRO N 284 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY N 300 " --> pdb=" O ILE N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 317 removed outlier: 5.198A pdb=" N ILE N 315 " --> pdb=" O ASP N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 319 through 326 Processing helix chain 'N' and resid 334 through 342 Processing helix chain 'N' and resid 347 through 358 Processing helix chain 'P' and resid 144 through 155 removed outlier: 3.732A pdb=" N THR P 153 " --> pdb=" O ASN P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 169 Processing helix chain 'P' and resid 173 through 182 Processing helix chain 'P' and resid 190 through 209 Processing helix chain 'P' and resid 227 through 232 removed outlier: 3.576A pdb=" N ARG P 232 " --> pdb=" O ALA P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 269 removed outlier: 3.631A pdb=" N ILE P 269 " --> pdb=" O ILE P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 300 removed outlier: 3.887A pdb=" N GLY P 300 " --> pdb=" O ILE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 302 through 314 Processing helix chain 'P' and resid 320 through 325 Processing helix chain 'P' and resid 334 through 342 Processing helix chain 'P' and resid 347 through 358 1716 hydrogen bonds defined for protein. 5148 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: 9.20 Time building geometry restraints manager: 12.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10468 1.34 - 1.46: 4894 1.46 - 1.58: 15850 1.58 - 1.70: 0 1.70 - 1.81: 378 Bond restraints: 31590 Sorted by residual: bond pdb=" C TYR M 285 " pdb=" N PRO M 286 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.12e+00 bond pdb=" C TYR D 285 " pdb=" N PRO D 286 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.09e+00 bond pdb=" CA TYR H 285 " pdb=" C TYR H 285 " ideal model delta sigma weight residual 1.521 1.538 -0.017 1.17e-02 7.31e+03 2.06e+00 bond pdb=" CA TYR Q 285 " pdb=" C TYR Q 285 " ideal model delta sigma weight residual 1.521 1.538 -0.016 1.17e-02 7.31e+03 1.93e+00 bond pdb=" CA TYR I 285 " pdb=" C TYR I 285 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.17e-02 7.31e+03 1.87e+00 ... (remaining 31585 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.25: 1217 106.25 - 113.21: 16646 113.21 - 120.16: 12542 120.16 - 127.12: 11936 127.12 - 134.08: 409 Bond angle restraints: 42750 Sorted by residual: angle pdb=" N VAL E 183 " pdb=" CA VAL E 183 " pdb=" C VAL E 183 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.18e+01 angle pdb=" N VAL J 183 " pdb=" CA VAL J 183 " pdb=" C VAL J 183 " ideal model delta sigma weight residual 113.53 108.99 4.54 9.80e-01 1.04e+00 2.15e+01 angle pdb=" N VAL M 183 " pdb=" CA VAL M 183 " pdb=" C VAL M 183 " ideal model delta sigma weight residual 113.53 108.99 4.54 9.80e-01 1.04e+00 2.14e+01 angle pdb=" N VAL N 183 " pdb=" CA VAL N 183 " pdb=" C VAL N 183 " ideal model delta sigma weight residual 113.53 109.00 4.53 9.80e-01 1.04e+00 2.14e+01 angle pdb=" N VAL A 183 " pdb=" CA VAL A 183 " pdb=" C VAL A 183 " ideal model delta sigma weight residual 113.53 109.01 4.52 9.80e-01 1.04e+00 2.13e+01 ... (remaining 42745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 16859 15.71 - 31.42: 2108 31.42 - 47.14: 532 47.14 - 62.85: 139 62.85 - 78.56: 36 Dihedral angle restraints: 19674 sinusoidal: 8370 harmonic: 11304 Sorted by residual: dihedral pdb=" CA PRO E 185 " pdb=" C PRO E 185 " pdb=" N GLY E 186 " pdb=" CA GLY E 186 " ideal model delta harmonic sigma weight residual -180.00 -148.16 -31.84 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA PRO A 185 " pdb=" C PRO A 185 " pdb=" N GLY A 186 " pdb=" CA GLY A 186 " ideal model delta harmonic sigma weight residual -180.00 -148.20 -31.80 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA PRO M 185 " pdb=" C PRO M 185 " pdb=" N GLY M 186 " pdb=" CA GLY M 186 " ideal model delta harmonic sigma weight residual -180.00 -148.20 -31.80 0 5.00e+00 4.00e-02 4.04e+01 ... (remaining 19671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3363 0.053 - 0.106: 1106 0.106 - 0.159: 166 0.159 - 0.212: 39 0.212 - 0.265: 6 Chirality restraints: 4680 Sorted by residual: chirality pdb=" CB VAL C 183 " pdb=" CA VAL C 183 " pdb=" CG1 VAL C 183 " pdb=" CG2 VAL C 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL L 183 " pdb=" CA VAL L 183 " pdb=" CG1 VAL L 183 " pdb=" CG2 VAL L 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL I 183 " pdb=" CA VAL I 183 " pdb=" CG1 VAL I 183 " pdb=" CG2 VAL I 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4677 not shown) Planarity restraints: 5688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 184 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO M 185 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO M 185 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO M 185 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 184 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO J 185 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO J 185 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 185 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 184 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO A 185 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " 0.034 5.00e-02 4.00e+02 ... (remaining 5685 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.33: 12 1.33 - 2.22: 22 2.22 - 3.12: 21816 3.12 - 4.01: 77255 4.01 - 4.90: 137956 Warning: very small nonbonded interaction distances. Nonbonded interactions: 237061 Sorted by model distance: nonbonded pdb=" N GLY A 143 " pdb=" NE2 GLN C 255 " model vdw 0.439 3.200 nonbonded pdb=" N GLY J 143 " pdb=" NE2 GLN L 255 " model vdw 0.439 3.200 nonbonded pdb=" NE2 GLN I 255 " pdb=" N GLY E 143 " model vdw 0.653 3.200 nonbonded pdb=" NE2 GLN R 255 " pdb=" N GLY N 143 " model vdw 0.653 3.200 nonbonded pdb=" N GLY D 143 " pdb=" NE2 GLN H 255 " model vdw 0.900 3.200 ... (remaining 237056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 19458 2.51 5 N 5472 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.750 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.240 Process input model: 72.920 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 31590 Z= 0.348 Angle : 0.850 7.830 42750 Z= 0.476 Chirality : 0.052 0.265 4680 Planarity : 0.007 0.062 5688 Dihedral : 15.280 78.560 12276 Min Nonbonded Distance : 0.439 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.05 % Favored : 92.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.10), residues: 3870 helix: -2.37 (0.07), residues: 2622 sheet: None (None), residues: 0 loop : -2.38 (0.16), residues: 1248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1653 time to evaluate : 3.489 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 outliers start: 0 outliers final: 0 residues processed: 1653 average time/residue: 0.4413 time to fit residues: 1118.5047 Evaluate side-chains 1202 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1202 time to evaluate : 3.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 343 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 163 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 328 HIS A 350 GLN B 158 ASN B 178 ASN B 190 GLN B 241 GLN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS C 149 ASN C 251 GLN C 276 ASN C 279 GLN F 158 ASN F 187 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN H 154 ASN H 207 ASN H 209 HIS H 241 GLN H 251 GLN H 276 ASN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 ASN I 248 GLN I 279 GLN E 163 ASN E 221 GLN E 295 GLN ** E 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN G 162 GLN G 178 ASN ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 ASN J 163 ASN ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 GLN J 350 GLN K 158 ASN K 178 ASN K 190 GLN K 241 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 HIS L 149 ASN L 251 GLN L 276 ASN L 279 GLN O 158 ASN O 187 GLN ** O 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 HIS ** M 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 154 ASN Q 207 ASN Q 209 HIS Q 241 GLN Q 251 GLN Q 276 ASN ** Q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN R 241 GLN R 248 GLN R 279 GLN N 163 ASN N 221 GLN N 295 GLN ** N 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 158 ASN P 178 ASN ** P 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 31590 Z= 0.301 Angle : 0.696 9.241 42750 Z= 0.359 Chirality : 0.045 0.197 4680 Planarity : 0.007 0.142 5688 Dihedral : 5.102 32.311 4194 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.41 % Favored : 93.44 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.24 (0.12), residues: 3870 helix: -0.24 (0.09), residues: 2628 sheet: None (None), residues: 0 loop : -1.95 (0.16), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1264 time to evaluate : 3.771 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 outliers start: 161 outliers final: 107 residues processed: 1334 average time/residue: 0.4084 time to fit residues: 858.7537 Evaluate side-chains 1269 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1162 time to evaluate : 3.670 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.2615 time to fit residues: 57.7346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 285 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 343 optimal weight: 20.0000 chunk 371 optimal weight: 30.0000 chunk 306 optimal weight: 0.9990 chunk 341 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 275 optimal weight: 0.0870 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN D 241 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 276 ASN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN J 192 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 GLN M 163 ASN M 241 GLN M 317 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 276 ASN N 350 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 31590 Z= 0.215 Angle : 0.629 8.215 42750 Z= 0.323 Chirality : 0.043 0.180 4680 Planarity : 0.006 0.105 5688 Dihedral : 4.862 30.189 4194 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.15 (0.13), residues: 3870 helix: 0.60 (0.10), residues: 2640 sheet: None (None), residues: 0 loop : -1.56 (0.17), residues: 1230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1281 time to evaluate : 3.727 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 outliers start: 75 outliers final: 34 residues processed: 1319 average time/residue: 0.4183 time to fit residues: 867.1604 Evaluate side-chains 1215 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1181 time to evaluate : 3.639 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2672 time to fit residues: 22.2344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 365 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 241 GLN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN H 276 ASN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 350 GLN E 350 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN ** G 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN M 255 GLN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 GLN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 31590 Z= 0.302 Angle : 0.667 8.615 42750 Z= 0.342 Chirality : 0.045 0.229 4680 Planarity : 0.006 0.106 5688 Dihedral : 4.806 29.226 4194 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.67 % Favored : 93.13 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3870 helix: 0.91 (0.10), residues: 2652 sheet: None (None), residues: 0 loop : -1.28 (0.18), residues: 1218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1222 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 90 residues processed: 1257 average time/residue: 0.4215 time to fit residues: 832.0507 Evaluate side-chains 1226 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1136 time to evaluate : 3.616 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.2858 time to fit residues: 51.9649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 272 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 chunk 327 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 350 GLN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN E 163 ASN E 301 HIS ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 HIS J 241 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 350 GLN Q 152 GLN N 162 GLN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 301 HIS N 350 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.118 31590 Z= 0.209 Angle : 0.628 9.160 42750 Z= 0.320 Chirality : 0.043 0.259 4680 Planarity : 0.006 0.110 5688 Dihedral : 4.665 29.373 4194 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3870 helix: 1.11 (0.10), residues: 2676 sheet: None (None), residues: 0 loop : -1.16 (0.18), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1250 time to evaluate : 3.732 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 outliers start: 56 outliers final: 27 residues processed: 1269 average time/residue: 0.4118 time to fit residues: 827.6983 Evaluate side-chains 1193 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1166 time to evaluate : 3.788 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2645 time to fit residues: 18.5514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 20.0000 chunk 329 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 214 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 365 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 HIS I 241 GLN E 162 GLN E 350 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 HIS N 162 GLN N 163 ASN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 31590 Z= 0.211 Angle : 0.650 10.788 42750 Z= 0.330 Chirality : 0.043 0.172 4680 Planarity : 0.007 0.127 5688 Dihedral : 4.566 26.373 4194 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.25 % Favored : 93.64 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3870 helix: 1.32 (0.10), residues: 2628 sheet: None (None), residues: 0 loop : -0.97 (0.18), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1221 time to evaluate : 3.815 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 outliers start: 69 outliers final: 45 residues processed: 1235 average time/residue: 0.4023 time to fit residues: 794.0264 Evaluate side-chains 1214 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1169 time to evaluate : 3.718 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2795 time to fit residues: 28.1040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 307 optimal weight: 0.5980 chunk 204 optimal weight: 8.9990 chunk 364 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 HIS I 276 ASN E 162 GLN E 303 GLN E 350 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 152 GLN Q 190 GLN Q 328 HIS R 276 ASN N 162 GLN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 303 GLN N 350 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 31590 Z= 0.244 Angle : 0.673 11.794 42750 Z= 0.341 Chirality : 0.043 0.184 4680 Planarity : 0.008 0.149 5688 Dihedral : 4.560 26.247 4194 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.77 % Favored : 93.13 % Rotamer Outliers : 1.69 % 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: 0.91 (0.14), residues: 3870 helix: 1.35 (0.10), residues: 2658 sheet: None (None), residues: 0 loop : -1.03 (0.18), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1211 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 35 residues processed: 1227 average time/residue: 0.3993 time to fit residues: 782.7478 Evaluate side-chains 1197 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1162 time to evaluate : 3.673 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2597 time to fit residues: 22.5163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 276 ASN Q 152 GLN N 162 GLN N 163 ASN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.147 31590 Z= 0.315 Angle : 0.722 11.160 42750 Z= 0.370 Chirality : 0.045 0.208 4680 Planarity : 0.008 0.135 5688 Dihedral : 4.643 25.855 4194 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.82 % Favored : 93.07 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3870 helix: 1.38 (0.10), residues: 2652 sheet: None (None), residues: 0 loop : -0.95 (0.19), residues: 1218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1174 time to evaluate : 3.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 48 residues processed: 1199 average time/residue: 0.4265 time to fit residues: 817.6408 Evaluate side-chains 1184 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1136 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2792 time to fit residues: 30.2425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 6.9990 chunk 349 optimal weight: 0.8980 chunk 318 optimal weight: 9.9990 chunk 339 optimal weight: 7.9990 chunk 348 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 266 optimal weight: 0.0170 chunk 104 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 321 optimal weight: 30.0000 overall best weight: 3.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN H 276 ASN E 350 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 HIS ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 276 ASN M 178 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 152 GLN N 162 GLN N 163 ASN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.154 31590 Z= 0.284 Angle : 0.721 12.178 42750 Z= 0.368 Chirality : 0.044 0.243 4680 Planarity : 0.008 0.148 5688 Dihedral : 4.633 27.356 4194 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.10 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3870 helix: 1.44 (0.10), residues: 2640 sheet: None (None), residues: 0 loop : -0.82 (0.19), residues: 1230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1176 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 1192 average time/residue: 0.4093 time to fit residues: 779.3918 Evaluate side-chains 1169 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1149 time to evaluate : 3.764 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2633 time to fit residues: 15.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 359 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 249 optimal weight: 0.0970 chunk 376 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 231 optimal weight: 8.9990 overall best weight: 2.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS C 276 ASN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 HIS ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 ASN L 276 ASN O 162 GLN M 350 GLN Q 152 GLN N 162 GLN N 163 ASN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.169 31590 Z= 0.294 Angle : 0.739 16.161 42750 Z= 0.385 Chirality : 0.044 0.255 4680 Planarity : 0.009 0.166 5688 Dihedral : 4.620 28.376 4194 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.69 % Favored : 93.18 % Rotamer Outliers : 0.68 % 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: 1.16 (0.14), residues: 3870 helix: 1.47 (0.10), residues: 2640 sheet: None (None), residues: 0 loop : -0.71 (0.19), residues: 1230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1174 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 1179 average time/residue: 0.4080 time to fit residues: 773.3152 Evaluate side-chains 1144 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1126 time to evaluate : 3.738 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2631 time to fit residues: 14.1849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 9.9990 chunk 238 optimal weight: 0.0000 chunk 319 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 276 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN C 276 ASN F 162 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 GLN L 276 ASN M 178 ASN ** R 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN ** P 190 GLN ** 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 = 0.3631 r_free = 0.3631 target = 0.138901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118680 restraints weight = 55866.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121496 restraints weight = 31927.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123353 restraints weight = 21316.105| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.174 31590 Z= 0.312 Angle : 0.761 17.536 42750 Z= 0.398 Chirality : 0.045 0.244 4680 Planarity : 0.009 0.179 5688 Dihedral : 4.581 26.009 4194 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.80 % Favored : 93.05 % Rotamer Outliers : 0.68 % 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: 1.22 (0.14), residues: 3870 helix: 1.51 (0.10), residues: 2640 sheet: None (None), residues: 0 loop : -0.70 (0.19), residues: 1230 =============================================================================== Job complete usr+sys time: 11140.07 seconds wall clock time: 197 minutes 34.16 seconds (11854.16 seconds total)