Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 10:02:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/04_2023/6a96_6998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/04_2023/6a96_6998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/04_2023/6a96_6998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/04_2023/6a96_6998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/04_2023/6a96_6998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a96_6998/04_2023/6a96_6998_updated.pdb" } resolution = 3.51 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= -0.023 sd= 0.837 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 160 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 11011 2.51 5 N 2753 2.21 5 O 3193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17049 Number of models: 1 Model: "" Number of chains: 19 Chain: "K" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 957 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "O" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2706 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Chain: "E" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "C" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.32, per 1000 atoms: 0.55 Number of scatterers: 17049 At special positions: 0 Unit cell: (130.54, 121.98, 144.45, 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 92 16.00 O 3193 8.00 N 2753 7.00 C 11011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.04 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 296 " distance=2.04 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " 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=6, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN A 114 " " NAG I 1 " - " ASN A 205 " " NAG J 1 " - " ASN E 149 " " NAG M 1 " - " ASN E 80 " " NAG N 1 " - " ASN C 149 " " NAG P 1 " - " ASN C 80 " " NAG Q 1 " - " ASN D 149 " " NAG R 1 " - " ASN D 80 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.67 Conformation dependent library (CDL) restraints added in 2.5 seconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 32 sheets defined 27.9% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 109 through 111 No H-bonds generated for 'chain 'L' and resid 109 through 111' Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'B' and resid 10 through 20 removed outlier: 4.124A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.622A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 250 through 266 removed outlier: 3.562A pdb=" N THR B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 280 through 305 removed outlier: 3.624A pdb=" N VAL B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 26 removed outlier: 3.508A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 226 through 249 removed outlier: 3.513A pdb=" N PHE A 229 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR A 234 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU A 235 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.861A pdb=" N MET A 239 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 246 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.954A pdb=" N VAL A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 311 removed outlier: 4.357A pdb=" N VAL A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 400 removed outlier: 4.171A pdb=" N ILE A 394 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP A 395 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 399 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 417 removed outlier: 3.767A pdb=" N LEU A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 20 removed outlier: 4.123A pdb=" N GLU E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.624A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 224 No H-bonds generated for 'chain 'E' and resid 221 through 224' Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 234 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 250 through 266 removed outlier: 3.561A pdb=" N THR E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 258 " --> pdb=" O GLY E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 280 through 305 removed outlier: 3.623A pdb=" N VAL E 292 " --> pdb=" O CYS E 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE E 305 " --> pdb=" O PHE E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 313 No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 removed outlier: 4.123A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.624A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 250 through 266 removed outlier: 3.561A pdb=" N THR C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 280 through 305 removed outlier: 3.624A pdb=" N VAL C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 removed outlier: 4.123A pdb=" N GLU D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.623A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 224 No H-bonds generated for 'chain 'D' and resid 221 through 224' Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.977A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 250 through 266 removed outlier: 3.561A pdb=" N THR D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 280 through 305 removed outlier: 3.622A pdb=" N VAL D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'D' and resid 423 through 427 Processing helix chain 'D' and resid 431 through 445 removed outlier: 4.668A pdb=" N SER D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.503A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 17 through 19 Processing sheet with id= C, first strand: chain 'K' and resid 97 through 99 removed outlier: 4.176A pdb=" N ILE K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET K 34 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 93 through 98 removed outlier: 3.950A pdb=" N MET L 34 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG L 38 " --> pdb=" O PHE L 47 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= F, first strand: chain 'O' and resid 3 through 7 Processing sheet with id= G, first strand: chain 'O' and resid 11 through 13 removed outlier: 6.544A pdb=" N THR O 122 " --> pdb=" O VAL O 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'O' and resid 96 through 99 removed outlier: 4.085A pdb=" N ILE O 33 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET O 34 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG O 38 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.718A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.868A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 147 through 155 removed outlier: 3.651A pdb=" N CYS B 150 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 212 " --> pdb=" O CYS B 150 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 191 through 199 removed outlier: 3.569A pdb=" N SER B 211 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 207 " --> pdb=" O ARG B 196 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.774A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 67 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 73 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR A 133 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 121 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 122 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 48 through 50 Processing sheet with id= P, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.897A pdb=" N THR A 200 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 107 through 112 removed outlier: 7.025A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.718A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.867A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 147 through 155 removed outlier: 3.650A pdb=" N CYS E 150 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE E 212 " --> pdb=" O CYS E 150 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 191 through 199 removed outlier: 3.570A pdb=" N SER E 211 " --> pdb=" O ARG E 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG E 207 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.717A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.868A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 147 through 155 removed outlier: 3.650A pdb=" N CYS C 150 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 212 " --> pdb=" O CYS C 150 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 191 through 199 removed outlier: 3.570A pdb=" N SER C 211 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 207 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 166 through 168 removed outlier: 6.717A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.867A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 147 through 155 removed outlier: 3.651A pdb=" N CYS D 150 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 212 " --> pdb=" O CYS D 150 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 191 through 199 removed outlier: 3.569A pdb=" N SER D 211 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG D 207 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 101 through 106 removed outlier: 7.098A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1386 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: 4.63 Time building geometry restraints manager: 8.75 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: 5173 1.34 - 1.46: 4848 1.46 - 1.59: 7306 1.59 - 1.71: 0 1.71 - 1.84: 158 Bond restraints: 17485 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 MAN H 4 " pdb=" C2 MAN H 4 " ideal model delta sigma weight residual 1.526 1.587 -0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" C5 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.418 1.474 -0.056 2.00e-02 2.50e+03 7.74e+00 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" C5 MAN J 5 " pdb=" O5 MAN J 5 " ideal model delta sigma weight residual 1.418 1.474 -0.056 2.00e-02 2.50e+03 7.70e+00 ... (remaining 17480 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.26: 334 105.26 - 112.49: 9045 112.49 - 119.72: 5817 119.72 - 126.95: 8364 126.95 - 134.18: 217 Bond angle restraints: 23777 Sorted by residual: angle pdb=" C LYS K 65 " pdb=" N ASP K 66 " pdb=" CA ASP K 66 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C MET A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CB MET A 115 " pdb=" CG MET A 115 " pdb=" SD MET A 115 " ideal model delta sigma weight residual 112.70 102.29 10.41 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 134.18 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C2 NAG Q 2 " pdb=" N2 NAG Q 2 " pdb=" C7 NAG Q 2 " ideal model delta sigma weight residual 124.56 134.05 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 23772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 9549 16.36 - 32.72: 309 32.72 - 49.08: 57 49.08 - 65.43: 4 65.43 - 81.79: 8 Dihedral angle restraints: 9927 sinusoidal: 3930 harmonic: 5997 Sorted by residual: dihedral pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " pdb=" SG CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sinusoidal sigma weight residual 93.00 141.02 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA PHE O 37 " pdb=" C PHE O 37 " pdb=" N ARG O 38 " pdb=" CA ARG O 38 " ideal model delta harmonic sigma weight residual 180.00 152.72 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TYR D 66 " pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 9924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2703 0.140 - 0.281: 48 0.281 - 0.421: 13 0.421 - 0.561: 1 0.561 - 0.701: 1 Chirality restraints: 2766 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 205 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL K 64 " pdb=" CA VAL K 64 " pdb=" CG1 VAL K 64 " pdb=" CG2 VAL K 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.09 -0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 2763 not shown) Planarity restraints: 2923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO B 432 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 431 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO D 432 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 432 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 431 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO E 432 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 432 " -0.039 5.00e-02 4.00e+02 ... (remaining 2920 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 749 2.71 - 3.25: 16092 3.25 - 3.80: 26963 3.80 - 4.35: 32162 4.35 - 4.90: 53246 Nonbonded interactions: 129212 Sorted by model distance: nonbonded pdb=" OG1 THR C 110 " pdb=" O THR D 96 " model vdw 2.158 2.440 nonbonded pdb=" OG1 THR B 110 " pdb=" O THR C 96 " model vdw 2.193 2.440 nonbonded pdb=" O2 BMA H 3 " pdb=" O6 MAN H 5 " model vdw 2.247 2.440 nonbonded pdb=" OG SER L 7 " pdb=" OG SER L 21 " model vdw 2.266 2.440 nonbonded pdb=" O PRO A 256 " pdb=" OG1 THR A 259 " model vdw 2.270 2.440 ... (remaining 129207 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 'B' and resid 8 through 447) selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'K' and resid 1 through 124) selection = chain 'L' selection = (chain 'O' and resid 1 through 124) } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 4.960 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 45.310 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.008 0.073 17485 Z= 0.506 Angle : 1.017 10.414 23777 Z= 0.504 Chirality : 0.063 0.701 2766 Planarity : 0.007 0.068 2913 Dihedral : 9.305 81.793 6072 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.16), residues: 2027 helix: -3.69 (0.13), residues: 395 sheet: -2.02 (0.21), residues: 551 loop : -2.17 (0.18), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 866 time to evaluate : 1.931 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 outliers start: 4 outliers final: 1 residues processed: 870 average time/residue: 0.3232 time to fit residues: 404.1212 Evaluate side-chains 485 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 484 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1541 time to fit residues: 3.1408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN O 30 ASN O 77 ASN A 317 GLN E 148 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN C 64 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 17485 Z= 0.241 Angle : 0.892 14.515 23777 Z= 0.423 Chirality : 0.051 0.396 2766 Planarity : 0.006 0.118 2913 Dihedral : 6.113 31.330 2297 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 4.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 2027 helix: -1.58 (0.21), residues: 437 sheet: -1.47 (0.21), residues: 549 loop : -1.68 (0.20), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 546 time to evaluate : 2.141 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 outliers start: 82 outliers final: 48 residues processed: 589 average time/residue: 0.3032 time to fit residues: 265.0255 Evaluate side-chains 515 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 467 time to evaluate : 1.914 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.1571 time to fit residues: 16.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 146 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN O 30 ASN B 191 HIS ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN C 64 GLN C 148 GLN D 191 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17485 Z= 0.194 Angle : 0.795 19.236 23777 Z= 0.371 Chirality : 0.048 0.366 2766 Planarity : 0.006 0.184 2913 Dihedral : 5.737 35.763 2297 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.97 (0.19), residues: 2027 helix: -0.73 (0.24), residues: 453 sheet: -1.12 (0.22), residues: 559 loop : -1.63 (0.20), residues: 1015 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 521 time to evaluate : 2.055 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: 48 outliers final: 20 residues processed: 544 average time/residue: 0.2888 time to fit residues: 235.3732 Evaluate side-chains 483 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 463 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1545 time to fit residues: 8.4650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN L 111 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 17485 Z= 0.283 Angle : 0.821 19.664 23777 Z= 0.381 Chirality : 0.048 0.349 2766 Planarity : 0.007 0.201 2913 Dihedral : 5.653 32.589 2297 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.84 (0.19), residues: 2027 helix: -0.49 (0.24), residues: 461 sheet: -1.03 (0.21), residues: 582 loop : -1.65 (0.20), residues: 984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 484 time to evaluate : 2.223 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 outliers start: 56 outliers final: 35 residues processed: 503 average time/residue: 0.2870 time to fit residues: 217.7171 Evaluate side-chains 484 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 449 time to evaluate : 2.007 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.1589 time to fit residues: 13.1817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17485 Z= 0.202 Angle : 0.791 15.390 23777 Z= 0.363 Chirality : 0.047 0.324 2766 Planarity : 0.005 0.142 2913 Dihedral : 5.441 33.954 2297 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.63 (0.19), residues: 2027 helix: -0.26 (0.24), residues: 461 sheet: -0.83 (0.22), residues: 571 loop : -1.59 (0.20), residues: 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 505 time to evaluate : 1.997 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 outliers start: 41 outliers final: 20 residues processed: 521 average time/residue: 0.2837 time to fit residues: 223.6652 Evaluate side-chains 477 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 457 time to evaluate : 2.089 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.2009 time to fit residues: 9.9110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN L 111 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 17485 Z= 0.277 Angle : 0.831 15.824 23777 Z= 0.384 Chirality : 0.048 0.302 2766 Planarity : 0.005 0.168 2913 Dihedral : 5.491 29.894 2297 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.69 (0.19), residues: 2027 helix: -0.44 (0.23), residues: 491 sheet: -0.76 (0.22), residues: 579 loop : -1.67 (0.21), residues: 957 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 465 time to evaluate : 2.021 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 outliers start: 51 outliers final: 38 residues processed: 485 average time/residue: 0.2792 time to fit residues: 203.9676 Evaluate side-chains 485 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 447 time to evaluate : 2.016 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.1816 time to fit residues: 14.5819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 0.0070 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 120 GLN L 111 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 17485 Z= 0.237 Angle : 0.820 15.224 23777 Z= 0.377 Chirality : 0.048 0.376 2766 Planarity : 0.006 0.175 2913 Dihedral : 5.418 29.790 2297 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.64 (0.19), residues: 2027 helix: -0.31 (0.24), residues: 493 sheet: -0.75 (0.22), residues: 528 loop : -1.64 (0.20), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 475 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 490 average time/residue: 0.2760 time to fit residues: 206.5648 Evaluate side-chains 475 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 458 time to evaluate : 1.811 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.1529 time to fit residues: 7.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 123 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 152 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS A 91 ASN A 278 ASN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 17485 Z= 0.186 Angle : 0.828 13.018 23777 Z= 0.377 Chirality : 0.047 0.286 2766 Planarity : 0.005 0.137 2913 Dihedral : 5.180 30.208 2297 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.38 (0.19), residues: 2027 helix: 0.01 (0.24), residues: 485 sheet: -0.69 (0.22), residues: 527 loop : -1.48 (0.20), residues: 1015 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 501 time to evaluate : 2.024 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 outliers start: 23 outliers final: 12 residues processed: 509 average time/residue: 0.2952 time to fit residues: 225.0212 Evaluate side-chains 474 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 462 time to evaluate : 2.086 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1643 time to fit residues: 6.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 118 optimal weight: 0.0050 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 17485 Z= 0.249 Angle : 0.857 17.177 23777 Z= 0.393 Chirality : 0.048 0.352 2766 Planarity : 0.005 0.128 2913 Dihedral : 5.282 25.899 2297 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.32 (0.19), residues: 2027 helix: 0.06 (0.24), residues: 482 sheet: -0.44 (0.23), residues: 517 loop : -1.56 (0.20), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 461 time to evaluate : 2.220 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 outliers start: 18 outliers final: 15 residues processed: 469 average time/residue: 0.2927 time to fit residues: 209.2764 Evaluate side-chains 457 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 442 time to evaluate : 2.099 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.1711 time to fit residues: 7.3704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 0.3980 chunk 116 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 chunk 132 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17485 Z= 0.208 Angle : 0.867 18.006 23777 Z= 0.395 Chirality : 0.048 0.294 2766 Planarity : 0.005 0.148 2913 Dihedral : 5.254 28.364 2297 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.27 (0.19), residues: 2027 helix: 0.07 (0.24), residues: 485 sheet: -0.33 (0.23), residues: 489 loop : -1.54 (0.20), residues: 1053 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 480 time to evaluate : 2.105 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 outliers start: 11 outliers final: 7 residues processed: 482 average time/residue: 0.2826 time to fit residues: 207.1924 Evaluate side-chains 460 residues out of total 1787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 453 time to evaluate : 2.216 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1554 time to fit residues: 4.7210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075014 restraints weight = 52609.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077678 restraints weight = 26301.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079490 restraints weight = 15831.932| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 17485 Z= 0.238 Angle : 0.887 16.348 23777 Z= 0.406 Chirality : 0.048 0.284 2766 Planarity : 0.008 0.343 2913 Dihedral : 5.375 44.342 2297 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % 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: -1.33 (0.19), residues: 2027 helix: -0.03 (0.24), residues: 497 sheet: -0.28 (0.24), residues: 489 loop : -1.62 (0.20), residues: 1041 =============================================================================== Job complete usr+sys time: 4393.72 seconds wall clock time: 80 minutes 1.75 seconds (4801.75 seconds total)