Starting phenix.real_space_refine on Fri Feb 16 03:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plp_20371/02_2024/6plp_20371_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plp_20371/02_2024/6plp_20371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plp_20371/02_2024/6plp_20371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plp_20371/02_2024/6plp_20371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plp_20371/02_2024/6plp_20371_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plp_20371/02_2024/6plp_20371_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.092 sd= 5.309 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9270 2.51 5 N 2290 2.21 5 O 2580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14240 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 7.33, per 1000 atoms: 0.51 Number of scatterers: 14240 At special positions: 0 Unit cell: (105.786, 107.745, 135.824, 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 100 16.00 O 2580 8.00 N 2290 7.00 C 9270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.19 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.19 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.19 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.19 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.19 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " 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 Links applied 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 2.5 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 20 sheets defined 35.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 236 through 242 removed outlier: 4.070A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 426 removed outlier: 3.646A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.233A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS A 426 " --> pdb=" O TRP A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 29 No H-bonds generated for 'chain 'B' and resid 26 through 29' Processing helix chain 'B' and resid 31 through 34 No H-bonds generated for 'chain 'B' and resid 31 through 34' Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 236 through 242 removed outlier: 4.070A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 426 removed outlier: 3.646A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.234A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 426 " --> pdb=" O TRP B 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 31 through 34 No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 236 through 242 removed outlier: 4.070A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 426 removed outlier: 3.647A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.234A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS C 426 " --> pdb=" O TRP C 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 29 No H-bonds generated for 'chain 'D' and resid 26 through 29' Processing helix chain 'D' and resid 31 through 34 No H-bonds generated for 'chain 'D' and resid 31 through 34' Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 236 through 242 removed outlier: 4.071A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 426 removed outlier: 3.647A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.233A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS D 426 " --> pdb=" O TRP D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 29 No H-bonds generated for 'chain 'E' and resid 26 through 29' Processing helix chain 'E' and resid 31 through 34 No H-bonds generated for 'chain 'E' and resid 31 through 34' Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 236 through 242 removed outlier: 4.069A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 286 removed outlier: 3.553A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 426 removed outlier: 3.647A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.233A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS E 426 " --> pdb=" O TRP E 422 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 228 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 227 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 165 through 167 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 228 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 227 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 165 through 167 Processing sheet with id= I, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 228 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 227 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 165 through 167 Processing sheet with id= M, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 228 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 227 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 165 through 167 Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 228 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 227 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 165 through 167 410 hydrogen bonds defined for protein. 1230 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: 4.23 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4385 1.34 - 1.46: 3523 1.46 - 1.58: 6507 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 550 107.32 - 113.99: 8264 113.99 - 120.66: 5763 120.66 - 127.33: 5037 127.33 - 133.99: 161 Bond angle restraints: 19775 Sorted by residual: angle pdb=" CB ABU C 504 " pdb=" CG ABU C 504 " pdb=" CD ABU C 504 " ideal model delta sigma weight residual 116.08 109.39 6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB ABU B 504 " pdb=" CG ABU B 504 " pdb=" CD ABU B 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.96e+00 angle pdb=" CB ABU A 504 " pdb=" CG ABU A 504 " pdb=" CD ABU A 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" CB ABU D 504 " pdb=" CG ABU D 504 " pdb=" CD ABU D 504 " ideal model delta sigma weight residual 116.08 109.43 6.65 3.00e+00 1.11e-01 4.91e+00 angle pdb=" CB ABU E 504 " pdb=" CG ABU E 504 " pdb=" CD ABU E 504 " ideal model delta sigma weight residual 116.08 109.44 6.64 3.00e+00 1.11e-01 4.90e+00 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8725 21.75 - 43.50: 150 43.50 - 65.24: 5 65.24 - 86.99: 30 86.99 - 108.74: 20 Dihedral angle restraints: 8930 sinusoidal: 3815 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.39 56.61 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.40 56.60 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2059 0.078 - 0.156: 196 0.156 - 0.235: 0 0.235 - 0.313: 5 0.313 - 0.391: 5 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.82e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 103 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.016 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4030 2.81 - 3.33: 12307 3.33 - 3.85: 21968 3.85 - 4.38: 27230 4.38 - 4.90: 45497 Nonbonded interactions: 111032 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.286 2.440 ... (remaining 111027 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' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.230 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.350 Find NCS groups from input model: 0.910 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 : 0.002 0.027 14585 Z= 0.133 Angle : 0.526 6.685 19775 Z= 0.258 Chirality : 0.046 0.391 2265 Planarity : 0.003 0.028 2450 Dihedral : 11.125 108.738 5580 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -4.40 (0.15), residues: 1710 helix: -4.20 (0.11), residues: 465 sheet: -2.53 (0.24), residues: 335 loop : -2.31 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 422 HIS 0.001 0.000 HIS C 125 PHE 0.003 0.001 PHE B 258 TYR 0.004 0.000 TYR D 74 ARG 0.002 0.000 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 1.552 Fit side-chains REVERT: A 71 THR cc_start: 0.8787 (p) cc_final: 0.8553 (p) REVERT: A 75 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.6824 (ttm110) REVERT: A 86 ASP cc_start: 0.8536 (t0) cc_final: 0.8315 (t70) REVERT: A 92 SER cc_start: 0.8643 (p) cc_final: 0.8373 (t) REVERT: A 96 ASP cc_start: 0.8389 (m-30) cc_final: 0.7836 (m-30) REVERT: A 105 MET cc_start: 0.7872 (mmm) cc_final: 0.7412 (ppp) REVERT: A 113 ASP cc_start: 0.8346 (p0) cc_final: 0.8011 (p0) REVERT: A 138 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8402 (mtpp) REVERT: A 163 MET cc_start: 0.6950 (mpp) cc_final: 0.6316 (mpp) REVERT: A 206 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7557 (mttt) REVERT: A 222 LYS cc_start: 0.6855 (ptmm) cc_final: 0.6487 (pttt) REVERT: A 291 PRO cc_start: 0.9313 (Cg_endo) cc_final: 0.9106 (Cg_exo) REVERT: A 295 TYR cc_start: 0.8200 (p90) cc_final: 0.7526 (p90) REVERT: A 398 ARG cc_start: 0.6573 (ttm170) cc_final: 0.6325 (ttm170) REVERT: B 45 ARG cc_start: 0.8660 (ptt90) cc_final: 0.8351 (ptm-80) REVERT: B 71 THR cc_start: 0.8691 (p) cc_final: 0.8475 (p) REVERT: B 96 ASP cc_start: 0.8398 (m-30) cc_final: 0.7744 (m-30) REVERT: B 105 MET cc_start: 0.7770 (mmm) cc_final: 0.7233 (ppp) REVERT: B 113 ASP cc_start: 0.8388 (p0) cc_final: 0.8069 (p0) REVERT: B 138 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8685 (mtmm) REVERT: B 163 MET cc_start: 0.6889 (mpp) cc_final: 0.6226 (mpp) REVERT: B 206 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7546 (mttt) REVERT: B 207 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8159 (tt0) REVERT: B 222 LYS cc_start: 0.7058 (ptmm) cc_final: 0.6646 (pttt) REVERT: B 295 TYR cc_start: 0.8299 (p90) cc_final: 0.7707 (p90) REVERT: B 398 ARG cc_start: 0.6530 (ttm170) cc_final: 0.6323 (ttm170) REVERT: C 75 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6814 (ttm110) REVERT: C 86 ASP cc_start: 0.8389 (t0) cc_final: 0.8173 (t70) REVERT: C 92 SER cc_start: 0.8730 (p) cc_final: 0.8441 (t) REVERT: C 96 ASP cc_start: 0.8480 (m-30) cc_final: 0.7855 (m-30) REVERT: C 105 MET cc_start: 0.7884 (mmm) cc_final: 0.7421 (ppp) REVERT: C 113 ASP cc_start: 0.8402 (p0) cc_final: 0.8080 (p0) REVERT: C 138 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8571 (mtpp) REVERT: C 163 MET cc_start: 0.7012 (mpp) cc_final: 0.6419 (mpp) REVERT: C 206 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7657 (mttt) REVERT: C 222 LYS cc_start: 0.7034 (ptmm) cc_final: 0.6639 (pttt) REVERT: C 233 GLU cc_start: 0.6920 (tt0) cc_final: 0.6692 (tt0) REVERT: C 291 PRO cc_start: 0.9322 (Cg_endo) cc_final: 0.9114 (Cg_exo) REVERT: C 295 TYR cc_start: 0.8259 (p90) cc_final: 0.7648 (p90) REVERT: C 398 ARG cc_start: 0.6656 (ttm170) cc_final: 0.6455 (ttm170) REVERT: D 75 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6856 (ttm110) REVERT: D 86 ASP cc_start: 0.8340 (t0) cc_final: 0.8113 (t70) REVERT: D 96 ASP cc_start: 0.8505 (m-30) cc_final: 0.7940 (m-30) REVERT: D 105 MET cc_start: 0.7785 (mmm) cc_final: 0.7166 (ppp) REVERT: D 138 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8566 (mtmm) REVERT: D 173 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6724 (mt-10) REVERT: D 206 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7327 (mttt) REVERT: D 233 GLU cc_start: 0.6784 (tt0) cc_final: 0.6554 (tt0) REVERT: D 295 TYR cc_start: 0.8356 (p90) cc_final: 0.7916 (p90) REVERT: D 398 ARG cc_start: 0.6617 (ttm170) cc_final: 0.6382 (ttm170) REVERT: E 45 ARG cc_start: 0.8761 (ptt90) cc_final: 0.8508 (ptm-80) REVERT: E 86 ASP cc_start: 0.8521 (t0) cc_final: 0.8292 (t70) REVERT: E 92 SER cc_start: 0.8564 (p) cc_final: 0.8259 (t) REVERT: E 96 ASP cc_start: 0.8477 (m-30) cc_final: 0.7979 (m-30) REVERT: E 105 MET cc_start: 0.7881 (mmm) cc_final: 0.7458 (ppp) REVERT: E 113 ASP cc_start: 0.8395 (p0) cc_final: 0.8067 (p0) REVERT: E 138 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8346 (mtpp) REVERT: E 206 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7398 (mttt) REVERT: E 291 PRO cc_start: 0.9285 (Cg_endo) cc_final: 0.9063 (Cg_exo) REVERT: E 295 TYR cc_start: 0.8289 (p90) cc_final: 0.7568 (p90) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.2601 time to fit residues: 184.9339 Evaluate side-chains 327 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 0.0050 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 overall best weight: 0.7874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 193 GLN A 202 GLN B 82 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN C 193 GLN C 202 GLN D 82 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 202 GLN E 261 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14585 Z= 0.175 Angle : 0.586 6.209 19775 Z= 0.293 Chirality : 0.045 0.197 2265 Planarity : 0.004 0.038 2450 Dihedral : 9.938 68.378 2200 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.65 % Allowed : 11.16 % Favored : 86.19 % 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: -3.22 (0.17), residues: 1710 helix: -2.26 (0.20), residues: 500 sheet: -1.81 (0.25), residues: 335 loop : -2.15 (0.17), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 302 HIS 0.002 0.001 HIS A 231 PHE 0.010 0.001 PHE E 311 TYR 0.012 0.001 TYR B 317 ARG 0.005 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 359 time to evaluate : 1.427 Fit side-chains REVERT: A 45 ARG cc_start: 0.8888 (ptt90) cc_final: 0.8543 (ptm-80) REVERT: A 71 THR cc_start: 0.8716 (p) cc_final: 0.8494 (p) REVERT: A 86 ASP cc_start: 0.8525 (t0) cc_final: 0.8270 (t70) REVERT: A 92 SER cc_start: 0.8647 (p) cc_final: 0.8304 (t) REVERT: A 96 ASP cc_start: 0.8262 (m-30) cc_final: 0.7880 (m-30) REVERT: A 105 MET cc_start: 0.7954 (mmm) cc_final: 0.7433 (ppp) REVERT: A 113 ASP cc_start: 0.8249 (p0) cc_final: 0.7834 (p0) REVERT: A 138 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8429 (mtpp) REVERT: A 179 MET cc_start: 0.7803 (mmm) cc_final: 0.7289 (mmm) REVERT: A 193 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: A 206 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7610 (mttt) REVERT: A 295 TYR cc_start: 0.8223 (p90) cc_final: 0.7607 (p90) REVERT: A 398 ARG cc_start: 0.6636 (ttm170) cc_final: 0.6352 (ttm170) REVERT: B 41 ASP cc_start: 0.8103 (t0) cc_final: 0.7879 (t0) REVERT: B 69 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 71 THR cc_start: 0.8610 (p) cc_final: 0.8403 (p) REVERT: B 96 ASP cc_start: 0.8227 (m-30) cc_final: 0.7790 (m-30) REVERT: B 105 MET cc_start: 0.7825 (mmm) cc_final: 0.7374 (ppp) REVERT: B 113 ASP cc_start: 0.8371 (p0) cc_final: 0.7978 (p0) REVERT: B 138 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8672 (mtmm) REVERT: B 163 MET cc_start: 0.6996 (mpp) cc_final: 0.6380 (mpp) REVERT: B 179 MET cc_start: 0.7786 (mmm) cc_final: 0.7282 (mmm) REVERT: B 295 TYR cc_start: 0.8320 (p90) cc_final: 0.7709 (p90) REVERT: B 398 ARG cc_start: 0.6578 (ttm170) cc_final: 0.6354 (ttm170) REVERT: B 422 TRP cc_start: 0.8285 (m100) cc_final: 0.7956 (m100) REVERT: C 28 GLU cc_start: 0.7133 (mp0) cc_final: 0.6901 (mp0) REVERT: C 45 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8568 (ptm160) REVERT: C 86 ASP cc_start: 0.8408 (t0) cc_final: 0.8196 (t70) REVERT: C 96 ASP cc_start: 0.8302 (m-30) cc_final: 0.7931 (m-30) REVERT: C 105 MET cc_start: 0.7932 (mmm) cc_final: 0.7559 (ppp) REVERT: C 138 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8579 (mtpp) REVERT: C 179 MET cc_start: 0.7861 (mmm) cc_final: 0.7332 (mmm) REVERT: C 206 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7645 (mttt) REVERT: C 250 ILE cc_start: 0.5076 (mm) cc_final: 0.4785 (mm) REVERT: C 295 TYR cc_start: 0.8310 (p90) cc_final: 0.7693 (p90) REVERT: C 398 ARG cc_start: 0.6751 (ttm170) cc_final: 0.6484 (ttm170) REVERT: D 28 GLU cc_start: 0.7301 (mp0) cc_final: 0.6803 (mp0) REVERT: D 45 ARG cc_start: 0.9004 (ptt90) cc_final: 0.8687 (ptm-80) REVERT: D 86 ASP cc_start: 0.8360 (t0) cc_final: 0.8104 (t70) REVERT: D 96 ASP cc_start: 0.8343 (m-30) cc_final: 0.7945 (m-30) REVERT: D 105 MET cc_start: 0.7861 (mmm) cc_final: 0.7158 (ppp) REVERT: D 138 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8559 (mtmm) REVERT: D 206 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7293 (mttm) REVERT: D 295 TYR cc_start: 0.8362 (p90) cc_final: 0.7997 (p90) REVERT: D 398 ARG cc_start: 0.6668 (ttm170) cc_final: 0.6359 (ttm170) REVERT: E 28 GLU cc_start: 0.7140 (mp0) cc_final: 0.6912 (mp0) REVERT: E 86 ASP cc_start: 0.8495 (t0) cc_final: 0.8281 (t70) REVERT: E 92 SER cc_start: 0.8537 (p) cc_final: 0.8171 (t) REVERT: E 96 ASP cc_start: 0.8380 (m-30) cc_final: 0.7969 (m-30) REVERT: E 105 MET cc_start: 0.7922 (mmm) cc_final: 0.7406 (ppp) REVERT: E 113 ASP cc_start: 0.8328 (p0) cc_final: 0.7925 (p0) REVERT: E 138 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8343 (mtpp) REVERT: E 139 ASN cc_start: 0.8756 (p0) cc_final: 0.8461 (p0) REVERT: E 170 MET cc_start: 0.8252 (ptp) cc_final: 0.7945 (ptp) REVERT: E 179 MET cc_start: 0.7767 (mmm) cc_final: 0.7537 (mmm) REVERT: E 206 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7568 (mttt) REVERT: E 295 TYR cc_start: 0.8287 (p90) cc_final: 0.7535 (p90) outliers start: 41 outliers final: 26 residues processed: 387 average time/residue: 0.2614 time to fit residues: 145.5498 Evaluate side-chains 341 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 275 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 0.0040 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 124 optimal weight: 6.9990 overall best weight: 0.5034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 193 GLN A 202 GLN B 202 GLN C 77 ASN C 82 GLN C 139 ASN C 202 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 202 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14585 Z= 0.139 Angle : 0.535 5.376 19775 Z= 0.260 Chirality : 0.044 0.186 2265 Planarity : 0.003 0.029 2450 Dihedral : 7.122 44.093 2200 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.84 % Allowed : 14.71 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 1710 helix: -1.21 (0.22), residues: 525 sheet: -1.47 (0.23), residues: 415 loop : -1.87 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 302 HIS 0.002 0.001 HIS A 125 PHE 0.008 0.001 PHE B 203 TYR 0.022 0.001 TYR C 317 ARG 0.004 0.000 ARG E 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 330 time to evaluate : 1.567 Fit side-chains REVERT: A 45 ARG cc_start: 0.8919 (ptt90) cc_final: 0.8599 (ptm-80) REVERT: A 86 ASP cc_start: 0.8545 (t0) cc_final: 0.8273 (t70) REVERT: A 92 SER cc_start: 0.8617 (p) cc_final: 0.8247 (t) REVERT: A 96 ASP cc_start: 0.8310 (m-30) cc_final: 0.7963 (m-30) REVERT: A 105 MET cc_start: 0.7984 (mmm) cc_final: 0.7351 (ppp) REVERT: A 113 ASP cc_start: 0.8230 (p0) cc_final: 0.7879 (p0) REVERT: A 138 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8323 (mtpp) REVERT: A 141 ASN cc_start: 0.8622 (m-40) cc_final: 0.8343 (m-40) REVERT: A 156 MET cc_start: 0.7678 (tpp) cc_final: 0.7356 (mmt) REVERT: A 193 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: A 206 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7525 (mttt) REVERT: A 295 TYR cc_start: 0.8210 (p90) cc_final: 0.7624 (p90) REVERT: A 398 ARG cc_start: 0.6616 (ttm170) cc_final: 0.6322 (ttm170) REVERT: B 69 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7829 (mm-30) REVERT: B 96 ASP cc_start: 0.8271 (m-30) cc_final: 0.7863 (m-30) REVERT: B 105 MET cc_start: 0.7847 (mmm) cc_final: 0.7387 (ppp) REVERT: B 113 ASP cc_start: 0.8322 (p0) cc_final: 0.7929 (p0) REVERT: B 138 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8627 (mtmm) REVERT: B 163 MET cc_start: 0.7118 (mpp) cc_final: 0.6517 (mpp) REVERT: B 179 MET cc_start: 0.7756 (mmm) cc_final: 0.7293 (mmm) REVERT: B 295 TYR cc_start: 0.8320 (p90) cc_final: 0.7694 (p90) REVERT: B 398 ARG cc_start: 0.6659 (ttm170) cc_final: 0.6361 (ttm170) REVERT: C 45 ARG cc_start: 0.8831 (ptm-80) cc_final: 0.8610 (ptm160) REVERT: C 72 MET cc_start: 0.8441 (mtt) cc_final: 0.8119 (mmm) REVERT: C 86 ASP cc_start: 0.8425 (t0) cc_final: 0.8188 (t70) REVERT: C 96 ASP cc_start: 0.8338 (m-30) cc_final: 0.7998 (m-30) REVERT: C 105 MET cc_start: 0.7957 (mmm) cc_final: 0.7553 (ppp) REVERT: C 138 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8472 (mtpp) REVERT: C 141 ASN cc_start: 0.8367 (m-40) cc_final: 0.8148 (m-40) REVERT: C 179 MET cc_start: 0.7894 (mmm) cc_final: 0.7440 (mmm) REVERT: C 206 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7650 (mttt) REVERT: C 250 ILE cc_start: 0.4963 (mm) cc_final: 0.4557 (mm) REVERT: C 295 TYR cc_start: 0.8311 (p90) cc_final: 0.7698 (p90) REVERT: C 398 ARG cc_start: 0.6791 (ttm170) cc_final: 0.6487 (ttm170) REVERT: D 28 GLU cc_start: 0.7390 (mp0) cc_final: 0.6855 (mp0) REVERT: D 45 ARG cc_start: 0.9010 (ptt90) cc_final: 0.8726 (ptm-80) REVERT: D 86 ASP cc_start: 0.8423 (t0) cc_final: 0.8152 (t70) REVERT: D 96 ASP cc_start: 0.8371 (m-30) cc_final: 0.7992 (m-30) REVERT: D 105 MET cc_start: 0.7870 (mmm) cc_final: 0.7252 (ppp) REVERT: D 138 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8462 (mtmm) REVERT: D 141 ASN cc_start: 0.8215 (m-40) cc_final: 0.7965 (m-40) REVERT: D 156 MET cc_start: 0.8384 (mmt) cc_final: 0.8129 (mmt) REVERT: D 206 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7338 (mttm) REVERT: D 295 TYR cc_start: 0.8336 (p90) cc_final: 0.8048 (p90) REVERT: D 398 ARG cc_start: 0.6639 (ttm170) cc_final: 0.6319 (ttm170) REVERT: E 28 GLU cc_start: 0.7197 (mp0) cc_final: 0.6879 (mp0) REVERT: E 45 ARG cc_start: 0.9011 (ptt90) cc_final: 0.8681 (ptm-80) REVERT: E 86 ASP cc_start: 0.8519 (t0) cc_final: 0.8127 (t70) REVERT: E 92 SER cc_start: 0.8519 (p) cc_final: 0.8174 (t) REVERT: E 96 ASP cc_start: 0.8400 (m-30) cc_final: 0.8031 (m-30) REVERT: E 105 MET cc_start: 0.7949 (mmm) cc_final: 0.7294 (ppp) REVERT: E 113 ASP cc_start: 0.8305 (p0) cc_final: 0.7928 (p0) REVERT: E 138 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8437 (mtpp) REVERT: E 139 ASN cc_start: 0.8731 (p0) cc_final: 0.8413 (p0) REVERT: E 156 MET cc_start: 0.8132 (mmt) cc_final: 0.7755 (mmt) REVERT: E 170 MET cc_start: 0.8229 (ptp) cc_final: 0.7977 (ptp) REVERT: E 179 MET cc_start: 0.7777 (mmm) cc_final: 0.7408 (mmm) REVERT: E 206 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7587 (mttt) REVERT: E 295 TYR cc_start: 0.8302 (p90) cc_final: 0.7540 (p90) outliers start: 44 outliers final: 30 residues processed: 367 average time/residue: 0.2424 time to fit residues: 131.7266 Evaluate side-chains 333 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 302 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 275 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14585 Z= 0.260 Angle : 0.573 5.366 19775 Z= 0.286 Chirality : 0.045 0.197 2265 Planarity : 0.004 0.036 2450 Dihedral : 5.256 38.087 2200 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.26 % Allowed : 15.87 % Favored : 79.87 % 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: -1.80 (0.19), residues: 1710 helix: -0.64 (0.23), residues: 525 sheet: -1.04 (0.26), residues: 380 loop : -1.57 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 302 HIS 0.003 0.001 HIS E 125 PHE 0.011 0.002 PHE C 417 TYR 0.015 0.002 TYR B 317 ARG 0.003 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 349 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8974 (ptt90) cc_final: 0.8622 (ptm-80) REVERT: A 86 ASP cc_start: 0.8746 (t0) cc_final: 0.8497 (t70) REVERT: A 96 ASP cc_start: 0.8341 (m-30) cc_final: 0.8028 (m-30) REVERT: A 105 MET cc_start: 0.8105 (mmm) cc_final: 0.7308 (ppp) REVERT: A 113 ASP cc_start: 0.8483 (p0) cc_final: 0.8103 (p0) REVERT: A 130 ASP cc_start: 0.8346 (m-30) cc_final: 0.8068 (m-30) REVERT: A 138 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8665 (mtpp) REVERT: A 141 ASN cc_start: 0.8632 (m-40) cc_final: 0.8272 (m-40) REVERT: A 156 MET cc_start: 0.7422 (tpp) cc_final: 0.6982 (mmt) REVERT: A 193 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: A 206 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7623 (mttt) REVERT: A 295 TYR cc_start: 0.8288 (p90) cc_final: 0.7877 (p90) REVERT: A 398 ARG cc_start: 0.6714 (ttm170) cc_final: 0.6331 (ttm170) REVERT: B 41 ASP cc_start: 0.8219 (t0) cc_final: 0.7969 (t0) REVERT: B 72 MET cc_start: 0.8383 (mmt) cc_final: 0.8037 (tpp) REVERT: B 96 ASP cc_start: 0.8298 (m-30) cc_final: 0.7976 (m-30) REVERT: B 105 MET cc_start: 0.8001 (mmm) cc_final: 0.7271 (ppp) REVERT: B 113 ASP cc_start: 0.8496 (p0) cc_final: 0.8084 (p0) REVERT: B 123 ASN cc_start: 0.8221 (p0) cc_final: 0.8015 (p0) REVERT: B 138 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8531 (mtmm) REVERT: B 179 MET cc_start: 0.7987 (mmm) cc_final: 0.7619 (mmm) REVERT: B 295 TYR cc_start: 0.8351 (p90) cc_final: 0.7869 (p90) REVERT: B 398 ARG cc_start: 0.6753 (ttm170) cc_final: 0.6391 (ttm170) REVERT: C 72 MET cc_start: 0.8481 (mtt) cc_final: 0.8155 (mmm) REVERT: C 96 ASP cc_start: 0.8335 (m-30) cc_final: 0.8035 (m-30) REVERT: C 105 MET cc_start: 0.8191 (mmm) cc_final: 0.7533 (ppp) REVERT: C 130 ASP cc_start: 0.8293 (m-30) cc_final: 0.8014 (m-30) REVERT: C 138 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8787 (mtpp) REVERT: C 179 MET cc_start: 0.8054 (mmm) cc_final: 0.7715 (mmm) REVERT: C 206 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7690 (mttt) REVERT: C 295 TYR cc_start: 0.8333 (p90) cc_final: 0.7841 (p90) REVERT: C 398 ARG cc_start: 0.6852 (ttm170) cc_final: 0.6471 (ttm170) REVERT: D 28 GLU cc_start: 0.7469 (mp0) cc_final: 0.6816 (mp0) REVERT: D 69 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7967 (mm-30) REVERT: D 70 THR cc_start: 0.8548 (m) cc_final: 0.8277 (p) REVERT: D 72 MET cc_start: 0.8407 (mmt) cc_final: 0.8196 (tpp) REVERT: D 96 ASP cc_start: 0.8392 (m-30) cc_final: 0.8005 (m-30) REVERT: D 105 MET cc_start: 0.8104 (mmm) cc_final: 0.7204 (ppp) REVERT: D 130 ASP cc_start: 0.8214 (m-30) cc_final: 0.7953 (m-30) REVERT: D 138 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8414 (mtmm) REVERT: D 156 MET cc_start: 0.8340 (mmt) cc_final: 0.8117 (mmt) REVERT: D 179 MET cc_start: 0.7828 (mmm) cc_final: 0.7318 (mmm) REVERT: D 206 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7390 (mttm) REVERT: D 398 ARG cc_start: 0.6658 (ttm170) cc_final: 0.6292 (ttm170) REVERT: E 45 ARG cc_start: 0.9058 (ptt90) cc_final: 0.8710 (ptm-80) REVERT: E 70 THR cc_start: 0.8670 (m) cc_final: 0.8383 (p) REVERT: E 92 SER cc_start: 0.8570 (p) cc_final: 0.8160 (t) REVERT: E 96 ASP cc_start: 0.8396 (m-30) cc_final: 0.8004 (m-30) REVERT: E 105 MET cc_start: 0.8048 (mmm) cc_final: 0.7279 (ppp) REVERT: E 113 ASP cc_start: 0.8523 (p0) cc_final: 0.8182 (p0) REVERT: E 130 ASP cc_start: 0.8283 (m-30) cc_final: 0.8043 (m-30) REVERT: E 138 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8622 (mtpp) REVERT: E 141 ASN cc_start: 0.8365 (m-40) cc_final: 0.8145 (m-40) REVERT: E 189 LYS cc_start: 0.7499 (ptpt) cc_final: 0.6909 (mptt) REVERT: E 206 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7597 (mttt) REVERT: E 295 TYR cc_start: 0.8266 (p90) cc_final: 0.7629 (p90) outliers start: 66 outliers final: 55 residues processed: 400 average time/residue: 0.2519 time to fit residues: 147.0340 Evaluate side-chains 375 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 319 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.0370 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 82 GLN C 202 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 77 ASN E 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14585 Z= 0.225 Angle : 0.557 9.131 19775 Z= 0.271 Chirality : 0.045 0.198 2265 Planarity : 0.003 0.052 2450 Dihedral : 4.738 26.673 2200 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.58 % Allowed : 17.10 % Favored : 78.32 % 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: -1.52 (0.20), residues: 1710 helix: -0.39 (0.24), residues: 525 sheet: -0.90 (0.27), residues: 380 loop : -1.40 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 186 HIS 0.003 0.001 HIS B 231 PHE 0.011 0.001 PHE A 309 TYR 0.016 0.001 TYR B 317 ARG 0.011 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 330 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8932 (ptt90) cc_final: 0.8627 (ptm-80) REVERT: A 96 ASP cc_start: 0.8337 (m-30) cc_final: 0.8047 (m-30) REVERT: A 105 MET cc_start: 0.8109 (mmm) cc_final: 0.7233 (ppp) REVERT: A 138 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8625 (mtmm) REVERT: A 141 ASN cc_start: 0.8588 (m-40) cc_final: 0.8172 (m-40) REVERT: A 156 MET cc_start: 0.7092 (tpp) cc_final: 0.6816 (mmt) REVERT: A 206 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7516 (mttt) REVERT: A 295 TYR cc_start: 0.8181 (p90) cc_final: 0.7834 (p90) REVERT: A 398 ARG cc_start: 0.6733 (ttm170) cc_final: 0.6317 (ttm170) REVERT: B 72 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8026 (mmt) REVERT: B 96 ASP cc_start: 0.8289 (m-30) cc_final: 0.7978 (m-30) REVERT: B 105 MET cc_start: 0.8078 (mmm) cc_final: 0.7215 (ppp) REVERT: B 113 ASP cc_start: 0.8631 (p0) cc_final: 0.8340 (p0) REVERT: B 138 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8501 (mtmm) REVERT: B 179 MET cc_start: 0.8034 (mmm) cc_final: 0.7578 (mmm) REVERT: B 295 TYR cc_start: 0.8324 (p90) cc_final: 0.7908 (p90) REVERT: B 398 ARG cc_start: 0.6777 (ttm170) cc_final: 0.6385 (ttm170) REVERT: C 72 MET cc_start: 0.8512 (mtt) cc_final: 0.8159 (mmm) REVERT: C 96 ASP cc_start: 0.8395 (m-30) cc_final: 0.8069 (m-30) REVERT: C 105 MET cc_start: 0.8226 (mmm) cc_final: 0.7484 (ppp) REVERT: C 130 ASP cc_start: 0.8325 (m-30) cc_final: 0.8034 (m-30) REVERT: C 138 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8485 (mtpp) REVERT: C 179 MET cc_start: 0.8118 (mmm) cc_final: 0.7717 (mmm) REVERT: C 206 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7595 (mttt) REVERT: C 295 TYR cc_start: 0.8305 (p90) cc_final: 0.7892 (p90) REVERT: C 398 ARG cc_start: 0.6856 (ttm170) cc_final: 0.6458 (ttm170) REVERT: D 28 GLU cc_start: 0.7494 (mp0) cc_final: 0.6955 (mp0) REVERT: D 45 ARG cc_start: 0.9125 (ptt90) cc_final: 0.8774 (ptm-80) REVERT: D 69 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8092 (mm-30) REVERT: D 70 THR cc_start: 0.8589 (m) cc_final: 0.8316 (p) REVERT: D 72 MET cc_start: 0.8451 (mmt) cc_final: 0.8116 (tpp) REVERT: D 96 ASP cc_start: 0.8361 (m-30) cc_final: 0.7994 (m-30) REVERT: D 100 ASP cc_start: 0.8152 (m-30) cc_final: 0.7907 (m-30) REVERT: D 105 MET cc_start: 0.8113 (mmm) cc_final: 0.7326 (ptm) REVERT: D 130 ASP cc_start: 0.8269 (m-30) cc_final: 0.7997 (m-30) REVERT: D 138 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8354 (mtmm) REVERT: D 139 ASN cc_start: 0.9013 (p0) cc_final: 0.8667 (p0) REVERT: D 156 MET cc_start: 0.8435 (mmt) cc_final: 0.8123 (mmt) REVERT: D 179 MET cc_start: 0.7841 (mmm) cc_final: 0.7267 (mmm) REVERT: D 206 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7336 (mttm) REVERT: D 398 ARG cc_start: 0.6632 (ttm170) cc_final: 0.6271 (ttm170) REVERT: E 45 ARG cc_start: 0.9036 (ptt90) cc_final: 0.8691 (ptm-80) REVERT: E 70 THR cc_start: 0.8672 (m) cc_final: 0.8372 (p) REVERT: E 72 MET cc_start: 0.8488 (mmt) cc_final: 0.8127 (mmm) REVERT: E 92 SER cc_start: 0.8578 (p) cc_final: 0.8157 (t) REVERT: E 96 ASP cc_start: 0.8387 (m-30) cc_final: 0.8052 (m-30) REVERT: E 105 MET cc_start: 0.8110 (mmm) cc_final: 0.7439 (ptm) REVERT: E 113 ASP cc_start: 0.8618 (p0) cc_final: 0.8295 (p0) REVERT: E 130 ASP cc_start: 0.8319 (m-30) cc_final: 0.8036 (m-30) REVERT: E 138 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8476 (mtpp) REVERT: E 206 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7327 (mttt) REVERT: E 222 LYS cc_start: 0.6705 (ptpt) cc_final: 0.6292 (pttt) REVERT: E 295 TYR cc_start: 0.8223 (p90) cc_final: 0.7540 (p90) outliers start: 71 outliers final: 48 residues processed: 384 average time/residue: 0.2640 time to fit residues: 148.9506 Evaluate side-chains 355 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 306 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN D 202 GLN D 261 ASN E 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14585 Z= 0.180 Angle : 0.535 8.396 19775 Z= 0.257 Chirality : 0.044 0.177 2265 Planarity : 0.003 0.031 2450 Dihedral : 4.402 20.801 2200 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.42 % Allowed : 18.52 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1710 helix: -0.12 (0.24), residues: 525 sheet: -0.74 (0.27), residues: 370 loop : -1.36 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 186 HIS 0.002 0.001 HIS B 231 PHE 0.011 0.001 PHE A 417 TYR 0.015 0.001 TYR B 317 ARG 0.009 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 315 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8895 (ptt90) cc_final: 0.8626 (ptm-80) REVERT: A 96 ASP cc_start: 0.8331 (m-30) cc_final: 0.8045 (m-30) REVERT: A 105 MET cc_start: 0.8095 (mmm) cc_final: 0.7200 (ppp) REVERT: A 123 ASN cc_start: 0.8384 (p0) cc_final: 0.8100 (p0) REVERT: A 138 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8617 (mtmm) REVERT: A 141 ASN cc_start: 0.8576 (m-40) cc_final: 0.8140 (m-40) REVERT: A 156 MET cc_start: 0.7199 (tpp) cc_final: 0.6628 (mmt) REVERT: A 179 MET cc_start: 0.7798 (mmm) cc_final: 0.7339 (mmm) REVERT: A 295 TYR cc_start: 0.8147 (p90) cc_final: 0.7715 (p90) REVERT: A 398 ARG cc_start: 0.6739 (ttm170) cc_final: 0.6296 (ttm170) REVERT: B 72 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8074 (tpp) REVERT: B 96 ASP cc_start: 0.8291 (m-30) cc_final: 0.7982 (m-30) REVERT: B 105 MET cc_start: 0.8024 (mmm) cc_final: 0.7090 (ppp) REVERT: B 113 ASP cc_start: 0.8640 (p0) cc_final: 0.8360 (p0) REVERT: B 138 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8414 (mtmm) REVERT: B 179 MET cc_start: 0.8043 (mmm) cc_final: 0.7569 (mmm) REVERT: B 295 TYR cc_start: 0.8297 (p90) cc_final: 0.7783 (p90) REVERT: B 398 ARG cc_start: 0.6761 (ttm170) cc_final: 0.6377 (ttm170) REVERT: C 72 MET cc_start: 0.8513 (mtt) cc_final: 0.8151 (mmm) REVERT: C 96 ASP cc_start: 0.8373 (m-30) cc_final: 0.8064 (m-30) REVERT: C 105 MET cc_start: 0.8243 (mmm) cc_final: 0.7465 (ppp) REVERT: C 130 ASP cc_start: 0.8299 (m-30) cc_final: 0.7965 (m-30) REVERT: C 138 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8445 (mtpp) REVERT: C 156 MET cc_start: 0.8323 (mmt) cc_final: 0.7902 (mmt) REVERT: C 179 MET cc_start: 0.8124 (mmm) cc_final: 0.7688 (mmm) REVERT: C 295 TYR cc_start: 0.8306 (p90) cc_final: 0.7966 (p90) REVERT: C 398 ARG cc_start: 0.6868 (ttm170) cc_final: 0.6453 (ttm170) REVERT: D 28 GLU cc_start: 0.7691 (mp0) cc_final: 0.6987 (mp0) REVERT: D 45 ARG cc_start: 0.9089 (ptt90) cc_final: 0.8772 (ptm-80) REVERT: D 69 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8094 (mm-30) REVERT: D 70 THR cc_start: 0.8604 (m) cc_final: 0.8332 (p) REVERT: D 72 MET cc_start: 0.8439 (mmt) cc_final: 0.8148 (tpp) REVERT: D 96 ASP cc_start: 0.8325 (m-30) cc_final: 0.7999 (m-30) REVERT: D 100 ASP cc_start: 0.8172 (m-30) cc_final: 0.7906 (m-30) REVERT: D 105 MET cc_start: 0.8088 (mmm) cc_final: 0.7433 (ptm) REVERT: D 130 ASP cc_start: 0.8257 (m-30) cc_final: 0.7957 (m-30) REVERT: D 138 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8253 (mtmm) REVERT: D 156 MET cc_start: 0.8452 (mmt) cc_final: 0.8115 (mmt) REVERT: D 206 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7422 (mttm) REVERT: D 254 SER cc_start: 0.8784 (m) cc_final: 0.8262 (p) REVERT: D 398 ARG cc_start: 0.6679 (ttm170) cc_final: 0.6291 (ttm170) REVERT: E 70 THR cc_start: 0.8655 (m) cc_final: 0.8351 (p) REVERT: E 72 MET cc_start: 0.8445 (mmt) cc_final: 0.8057 (mmm) REVERT: E 96 ASP cc_start: 0.8386 (m-30) cc_final: 0.8060 (m-30) REVERT: E 105 MET cc_start: 0.8052 (mmm) cc_final: 0.7404 (ptm) REVERT: E 113 ASP cc_start: 0.8615 (p0) cc_final: 0.8300 (p0) REVERT: E 130 ASP cc_start: 0.8320 (m-30) cc_final: 0.7970 (m-30) REVERT: E 138 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8535 (mtpp) REVERT: E 295 TYR cc_start: 0.8201 (p90) cc_final: 0.7514 (p90) outliers start: 53 outliers final: 39 residues processed: 357 average time/residue: 0.2446 time to fit residues: 129.5978 Evaluate side-chains 339 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 299 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 82 GLN B 202 GLN C 202 GLN D 202 GLN D 261 ASN E 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14585 Z= 0.370 Angle : 0.641 8.678 19775 Z= 0.314 Chirality : 0.047 0.178 2265 Planarity : 0.004 0.034 2450 Dihedral : 4.743 21.140 2200 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.45 % Allowed : 17.74 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1710 helix: -0.35 (0.23), residues: 525 sheet: -0.83 (0.27), residues: 385 loop : -1.23 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 186 HIS 0.004 0.002 HIS B 231 PHE 0.015 0.002 PHE A 309 TYR 0.016 0.002 TYR B 317 ARG 0.010 0.001 ARG C 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 331 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8106 (mmm) cc_final: 0.7336 (ptm) REVERT: A 123 ASN cc_start: 0.8453 (p0) cc_final: 0.8188 (p0) REVERT: A 138 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8638 (mtmm) REVERT: A 141 ASN cc_start: 0.8577 (m-40) cc_final: 0.8235 (m-40) REVERT: A 156 MET cc_start: 0.7380 (tpp) cc_final: 0.6960 (mmt) REVERT: A 179 MET cc_start: 0.8049 (mmm) cc_final: 0.7545 (mmm) REVERT: A 216 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6545 (ptpt) REVERT: A 292 LYS cc_start: 0.8383 (mttt) cc_final: 0.7857 (mttm) REVERT: A 295 TYR cc_start: 0.8244 (p90) cc_final: 0.7924 (p90) REVERT: A 398 ARG cc_start: 0.6745 (ttm170) cc_final: 0.6236 (ttm170) REVERT: B 41 ASP cc_start: 0.8237 (t0) cc_final: 0.8006 (t0) REVERT: B 72 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8134 (mmt) REVERT: B 105 MET cc_start: 0.8086 (mmm) cc_final: 0.7395 (ptm) REVERT: B 113 ASP cc_start: 0.8778 (p0) cc_final: 0.8509 (p0) REVERT: B 138 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8466 (mtmm) REVERT: B 179 MET cc_start: 0.8113 (mmm) cc_final: 0.7761 (mmm) REVERT: B 254 SER cc_start: 0.8904 (m) cc_final: 0.8402 (p) REVERT: B 292 LYS cc_start: 0.8490 (mttt) cc_final: 0.8085 (mttm) REVERT: B 295 TYR cc_start: 0.8338 (p90) cc_final: 0.7915 (p90) REVERT: B 398 ARG cc_start: 0.6790 (ttm170) cc_final: 0.6376 (ttm170) REVERT: C 41 ASP cc_start: 0.8144 (t0) cc_final: 0.7917 (t0) REVERT: C 70 THR cc_start: 0.8615 (m) cc_final: 0.8306 (p) REVERT: C 105 MET cc_start: 0.8261 (mmm) cc_final: 0.7421 (ppp) REVERT: C 130 ASP cc_start: 0.8430 (m-30) cc_final: 0.8130 (m-30) REVERT: C 138 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8714 (mtpp) REVERT: C 156 MET cc_start: 0.8391 (mmt) cc_final: 0.8124 (mmt) REVERT: C 179 MET cc_start: 0.8183 (mmm) cc_final: 0.7888 (mmm) REVERT: C 188 GLU cc_start: 0.8568 (mp0) cc_final: 0.8345 (pm20) REVERT: C 398 ARG cc_start: 0.6875 (ttm170) cc_final: 0.6468 (ttm170) REVERT: D 70 THR cc_start: 0.8674 (m) cc_final: 0.8367 (p) REVERT: D 72 MET cc_start: 0.8519 (mmt) cc_final: 0.8167 (tpp) REVERT: D 96 ASP cc_start: 0.8360 (m-30) cc_final: 0.8038 (m-30) REVERT: D 105 MET cc_start: 0.8137 (mmm) cc_final: 0.7382 (ptm) REVERT: D 130 ASP cc_start: 0.8379 (m-30) cc_final: 0.8091 (m-30) REVERT: D 138 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8329 (mtmm) REVERT: D 156 MET cc_start: 0.8523 (mmt) cc_final: 0.8159 (mmt) REVERT: D 179 MET cc_start: 0.8018 (mmm) cc_final: 0.7595 (mmm) REVERT: D 206 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7588 (mttt) REVERT: D 254 SER cc_start: 0.8799 (m) cc_final: 0.8278 (p) REVERT: D 279 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.4945 (ttm) REVERT: D 292 LYS cc_start: 0.8387 (mttt) cc_final: 0.8080 (mttm) REVERT: D 398 ARG cc_start: 0.6688 (ttm170) cc_final: 0.6264 (ttm170) REVERT: E 70 THR cc_start: 0.8740 (m) cc_final: 0.8417 (p) REVERT: E 96 ASP cc_start: 0.8391 (m-30) cc_final: 0.8037 (m-30) REVERT: E 105 MET cc_start: 0.8106 (mmm) cc_final: 0.7470 (ptm) REVERT: E 113 ASP cc_start: 0.8791 (p0) cc_final: 0.8465 (p0) REVERT: E 130 ASP cc_start: 0.8426 (m-30) cc_final: 0.8045 (m-30) REVERT: E 138 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8475 (mtpp) REVERT: E 295 TYR cc_start: 0.8241 (p90) cc_final: 0.7671 (p90) outliers start: 69 outliers final: 58 residues processed: 384 average time/residue: 0.2582 time to fit residues: 144.9657 Evaluate side-chains 378 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 317 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 111 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN D 202 GLN D 261 ASN E 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14585 Z= 0.158 Angle : 0.549 8.091 19775 Z= 0.265 Chirality : 0.043 0.166 2265 Planarity : 0.003 0.030 2450 Dihedral : 4.387 19.385 2200 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.16 % Allowed : 19.68 % Favored : 77.16 % 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: -1.03 (0.21), residues: 1710 helix: 0.08 (0.25), residues: 495 sheet: -0.74 (0.27), residues: 370 loop : -1.05 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 186 HIS 0.001 0.001 HIS C 217 PHE 0.012 0.001 PHE A 417 TYR 0.015 0.001 TYR C 317 ARG 0.008 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 317 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8908 (ptt90) cc_final: 0.8644 (ptm-80) REVERT: A 86 ASP cc_start: 0.8973 (t0) cc_final: 0.8658 (t70) REVERT: A 105 MET cc_start: 0.8011 (mmm) cc_final: 0.7275 (ptm) REVERT: A 123 ASN cc_start: 0.8494 (p0) cc_final: 0.8228 (p0) REVERT: A 138 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8624 (mtmm) REVERT: A 141 ASN cc_start: 0.8522 (m-40) cc_final: 0.8253 (m-40) REVERT: A 156 MET cc_start: 0.7219 (tpp) cc_final: 0.6726 (mmt) REVERT: A 179 MET cc_start: 0.7903 (mmm) cc_final: 0.7419 (mmm) REVERT: A 292 LYS cc_start: 0.8245 (mttt) cc_final: 0.7758 (mttm) REVERT: A 295 TYR cc_start: 0.8201 (p90) cc_final: 0.7766 (p90) REVERT: A 398 ARG cc_start: 0.6722 (ttm170) cc_final: 0.6228 (ttm170) REVERT: B 45 ARG cc_start: 0.8966 (ptt90) cc_final: 0.8536 (ptm-80) REVERT: B 72 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8142 (tpp) REVERT: B 105 MET cc_start: 0.8051 (mmm) cc_final: 0.7375 (ptm) REVERT: B 113 ASP cc_start: 0.8715 (p0) cc_final: 0.8429 (p0) REVERT: B 138 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8349 (mtmm) REVERT: B 179 MET cc_start: 0.8076 (mmm) cc_final: 0.7767 (mmm) REVERT: B 295 TYR cc_start: 0.8258 (p90) cc_final: 0.7815 (p90) REVERT: B 398 ARG cc_start: 0.6796 (ttm170) cc_final: 0.6385 (ttm170) REVERT: C 41 ASP cc_start: 0.8044 (t0) cc_final: 0.7808 (t0) REVERT: C 70 THR cc_start: 0.8567 (m) cc_final: 0.8262 (p) REVERT: C 105 MET cc_start: 0.8195 (mmm) cc_final: 0.7390 (ppp) REVERT: C 130 ASP cc_start: 0.8354 (m-30) cc_final: 0.8021 (m-30) REVERT: C 138 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8662 (mtpp) REVERT: C 156 MET cc_start: 0.8267 (mmt) cc_final: 0.7963 (mmt) REVERT: C 179 MET cc_start: 0.8223 (mmm) cc_final: 0.7878 (mmm) REVERT: C 279 MET cc_start: 0.5821 (ttm) cc_final: 0.5472 (ttm) REVERT: C 287 ARG cc_start: 0.7334 (ptp-170) cc_final: 0.7132 (ptp-170) REVERT: C 398 ARG cc_start: 0.6846 (ttm170) cc_final: 0.6438 (ttm170) REVERT: C 416 ILE cc_start: 0.8229 (mt) cc_final: 0.7945 (tp) REVERT: D 70 THR cc_start: 0.8631 (m) cc_final: 0.8361 (p) REVERT: D 72 MET cc_start: 0.8513 (mmt) cc_final: 0.8223 (tpp) REVERT: D 96 ASP cc_start: 0.8294 (m-30) cc_final: 0.7965 (m-30) REVERT: D 105 MET cc_start: 0.8116 (mmm) cc_final: 0.7369 (ptm) REVERT: D 130 ASP cc_start: 0.8306 (m-30) cc_final: 0.8008 (m-30) REVERT: D 138 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8476 (mtpp) REVERT: D 141 ASN cc_start: 0.8257 (m-40) cc_final: 0.8035 (m-40) REVERT: D 156 MET cc_start: 0.8451 (mmt) cc_final: 0.8062 (mmt) REVERT: D 179 MET cc_start: 0.7931 (mmm) cc_final: 0.7467 (mmm) REVERT: D 206 LYS cc_start: 0.7867 (mtpt) cc_final: 0.7282 (mttm) REVERT: D 254 SER cc_start: 0.8810 (m) cc_final: 0.8315 (p) REVERT: D 279 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5169 (ttm) REVERT: D 398 ARG cc_start: 0.6713 (ttm170) cc_final: 0.6275 (ttm170) REVERT: E 45 ARG cc_start: 0.9006 (ptt90) cc_final: 0.8718 (ptm-80) REVERT: E 70 THR cc_start: 0.8708 (m) cc_final: 0.8404 (p) REVERT: E 72 MET cc_start: 0.8450 (tpp) cc_final: 0.8095 (tpp) REVERT: E 96 ASP cc_start: 0.8354 (m-30) cc_final: 0.8027 (m-30) REVERT: E 105 MET cc_start: 0.8050 (mmm) cc_final: 0.7453 (ptm) REVERT: E 113 ASP cc_start: 0.8711 (p0) cc_final: 0.8407 (p0) REVERT: E 130 ASP cc_start: 0.8347 (m-30) cc_final: 0.7963 (m-30) REVERT: E 138 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8531 (mtpp) REVERT: E 292 LYS cc_start: 0.8294 (mttt) cc_final: 0.7347 (mttp) REVERT: E 295 TYR cc_start: 0.8181 (p90) cc_final: 0.7576 (p90) outliers start: 49 outliers final: 38 residues processed: 349 average time/residue: 0.2629 time to fit residues: 133.4887 Evaluate side-chains 353 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 313 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN E 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14585 Z= 0.222 Angle : 0.566 9.378 19775 Z= 0.274 Chirality : 0.044 0.155 2265 Planarity : 0.003 0.035 2450 Dihedral : 4.399 19.011 2200 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.90 % Allowed : 20.13 % Favored : 76.97 % 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: -0.99 (0.20), residues: 1710 helix: 0.11 (0.25), residues: 495 sheet: -0.70 (0.26), residues: 380 loop : -1.03 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 186 HIS 0.002 0.001 HIS B 231 PHE 0.013 0.001 PHE A 417 TYR 0.014 0.001 TYR B 317 ARG 0.008 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 319 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8899 (ptt90) cc_final: 0.8665 (ptm-80) REVERT: A 105 MET cc_start: 0.8026 (mmm) cc_final: 0.7267 (ptm) REVERT: A 123 ASN cc_start: 0.8499 (p0) cc_final: 0.8231 (p0) REVERT: A 138 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8601 (mtmm) REVERT: A 141 ASN cc_start: 0.8510 (m-40) cc_final: 0.8219 (m-40) REVERT: A 156 MET cc_start: 0.7517 (tpp) cc_final: 0.7039 (mmt) REVERT: A 179 MET cc_start: 0.7947 (mmm) cc_final: 0.7454 (mmm) REVERT: A 292 LYS cc_start: 0.8294 (mttt) cc_final: 0.7817 (mttm) REVERT: A 295 TYR cc_start: 0.8265 (p90) cc_final: 0.7873 (p90) REVERT: A 398 ARG cc_start: 0.6719 (ttm170) cc_final: 0.6218 (ttm170) REVERT: B 41 ASP cc_start: 0.8185 (t0) cc_final: 0.7969 (t0) REVERT: B 72 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8117 (tpp) REVERT: B 105 MET cc_start: 0.8036 (mmm) cc_final: 0.7357 (ptm) REVERT: B 113 ASP cc_start: 0.8722 (p0) cc_final: 0.8439 (p0) REVERT: B 138 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8354 (mtpp) REVERT: B 179 MET cc_start: 0.8159 (mmm) cc_final: 0.7758 (mmm) REVERT: B 295 TYR cc_start: 0.8292 (p90) cc_final: 0.7795 (p90) REVERT: B 398 ARG cc_start: 0.6814 (ttm170) cc_final: 0.6386 (ttm170) REVERT: C 41 ASP cc_start: 0.8072 (t0) cc_final: 0.7825 (t0) REVERT: C 70 THR cc_start: 0.8566 (m) cc_final: 0.8260 (p) REVERT: C 105 MET cc_start: 0.8191 (mmm) cc_final: 0.7356 (ppp) REVERT: C 130 ASP cc_start: 0.8371 (m-30) cc_final: 0.8031 (m-30) REVERT: C 138 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8554 (mtpp) REVERT: C 156 MET cc_start: 0.8368 (mmt) cc_final: 0.8003 (mmt) REVERT: C 179 MET cc_start: 0.8168 (mmm) cc_final: 0.7839 (mmm) REVERT: C 188 GLU cc_start: 0.8510 (mp0) cc_final: 0.8091 (pm20) REVERT: C 292 LYS cc_start: 0.8364 (mttt) cc_final: 0.7919 (mttm) REVERT: C 398 ARG cc_start: 0.6880 (ttm170) cc_final: 0.6443 (ttm170) REVERT: C 416 ILE cc_start: 0.8242 (mt) cc_final: 0.7984 (tp) REVERT: D 70 THR cc_start: 0.8672 (m) cc_final: 0.8394 (p) REVERT: D 72 MET cc_start: 0.8513 (mmt) cc_final: 0.8228 (tpp) REVERT: D 96 ASP cc_start: 0.8275 (m-30) cc_final: 0.7943 (m-30) REVERT: D 105 MET cc_start: 0.8097 (mmm) cc_final: 0.7345 (ptm) REVERT: D 130 ASP cc_start: 0.8347 (m-30) cc_final: 0.8035 (m-30) REVERT: D 138 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8509 (mtpp) REVERT: D 156 MET cc_start: 0.8483 (mmt) cc_final: 0.8072 (mmt) REVERT: D 179 MET cc_start: 0.7961 (mmm) cc_final: 0.7482 (mmm) REVERT: D 206 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7312 (mttm) REVERT: D 254 SER cc_start: 0.8802 (m) cc_final: 0.8300 (p) REVERT: D 279 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.5041 (ttm) REVERT: D 292 LYS cc_start: 0.8402 (mttt) cc_final: 0.8047 (mttm) REVERT: D 398 ARG cc_start: 0.6742 (ttm170) cc_final: 0.6289 (ttm170) REVERT: E 45 ARG cc_start: 0.8999 (ptt90) cc_final: 0.8723 (ptm-80) REVERT: E 70 THR cc_start: 0.8713 (m) cc_final: 0.8410 (p) REVERT: E 72 MET cc_start: 0.8463 (tpp) cc_final: 0.8091 (tpp) REVERT: E 96 ASP cc_start: 0.8362 (m-30) cc_final: 0.8020 (m-30) REVERT: E 105 MET cc_start: 0.8056 (mmm) cc_final: 0.7420 (ptm) REVERT: E 113 ASP cc_start: 0.8715 (p0) cc_final: 0.8374 (p0) REVERT: E 130 ASP cc_start: 0.8388 (m-30) cc_final: 0.7991 (m-30) REVERT: E 138 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8548 (mtpp) REVERT: E 292 LYS cc_start: 0.8411 (mttt) cc_final: 0.7983 (mttp) REVERT: E 295 TYR cc_start: 0.8270 (p90) cc_final: 0.7604 (p90) outliers start: 45 outliers final: 42 residues processed: 350 average time/residue: 0.2532 time to fit residues: 129.9111 Evaluate side-chains 354 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 310 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.0010 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN E 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14585 Z= 0.232 Angle : 0.583 9.643 19775 Z= 0.282 Chirality : 0.044 0.151 2265 Planarity : 0.003 0.035 2450 Dihedral : 4.447 19.744 2200 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.84 % Allowed : 20.32 % Favored : 76.84 % 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: -0.94 (0.20), residues: 1710 helix: 0.06 (0.24), residues: 500 sheet: -0.68 (0.26), residues: 380 loop : -0.93 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 186 HIS 0.003 0.001 HIS B 231 PHE 0.013 0.001 PHE A 417 TYR 0.015 0.001 TYR B 317 ARG 0.007 0.001 ARG E 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 316 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8041 (mmm) cc_final: 0.7246 (ptm) REVERT: A 123 ASN cc_start: 0.8506 (p0) cc_final: 0.8242 (p0) REVERT: A 138 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8561 (mtmm) REVERT: A 141 ASN cc_start: 0.8509 (m-40) cc_final: 0.8223 (m-40) REVERT: A 156 MET cc_start: 0.7597 (tpp) cc_final: 0.6992 (mmt) REVERT: A 179 MET cc_start: 0.7942 (mmm) cc_final: 0.7711 (mmm) REVERT: A 243 MET cc_start: 0.7725 (mtm) cc_final: 0.7247 (ttm) REVERT: A 292 LYS cc_start: 0.8309 (mttt) cc_final: 0.7837 (mttm) REVERT: A 295 TYR cc_start: 0.8286 (p90) cc_final: 0.7831 (p90) REVERT: A 398 ARG cc_start: 0.6785 (ttm170) cc_final: 0.6263 (ttm170) REVERT: B 41 ASP cc_start: 0.8192 (t0) cc_final: 0.7968 (t0) REVERT: B 72 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8135 (tpp) REVERT: B 105 MET cc_start: 0.8033 (mmm) cc_final: 0.7330 (ptm) REVERT: B 113 ASP cc_start: 0.8747 (p0) cc_final: 0.8464 (p0) REVERT: B 138 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8348 (mtpp) REVERT: B 179 MET cc_start: 0.8157 (mmm) cc_final: 0.7751 (mmm) REVERT: B 292 LYS cc_start: 0.8510 (mttt) cc_final: 0.8193 (mttm) REVERT: B 295 TYR cc_start: 0.8291 (p90) cc_final: 0.7800 (p90) REVERT: B 398 ARG cc_start: 0.6832 (ttm170) cc_final: 0.6389 (ttm170) REVERT: C 41 ASP cc_start: 0.8075 (t0) cc_final: 0.7824 (t0) REVERT: C 70 THR cc_start: 0.8568 (m) cc_final: 0.8267 (p) REVERT: C 105 MET cc_start: 0.8191 (mmm) cc_final: 0.7359 (ppp) REVERT: C 130 ASP cc_start: 0.8369 (m-30) cc_final: 0.8018 (m-30) REVERT: C 156 MET cc_start: 0.8428 (mmt) cc_final: 0.7996 (mmt) REVERT: C 179 MET cc_start: 0.8196 (mmm) cc_final: 0.7893 (mmm) REVERT: C 398 ARG cc_start: 0.6901 (ttm170) cc_final: 0.6437 (ttm170) REVERT: C 416 ILE cc_start: 0.8233 (mt) cc_final: 0.7976 (tp) REVERT: D 70 THR cc_start: 0.8695 (m) cc_final: 0.8413 (p) REVERT: D 72 MET cc_start: 0.8523 (mmt) cc_final: 0.8320 (tpp) REVERT: D 96 ASP cc_start: 0.8276 (m-30) cc_final: 0.7943 (m-30) REVERT: D 105 MET cc_start: 0.7967 (mmm) cc_final: 0.7334 (ptm) REVERT: D 130 ASP cc_start: 0.8359 (m-30) cc_final: 0.8046 (m-30) REVERT: D 138 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8508 (mtpp) REVERT: D 156 MET cc_start: 0.8487 (mmt) cc_final: 0.8059 (mmt) REVERT: D 179 MET cc_start: 0.7952 (mmm) cc_final: 0.7460 (mmm) REVERT: D 206 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7309 (mttm) REVERT: D 254 SER cc_start: 0.8797 (m) cc_final: 0.8291 (p) REVERT: D 279 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.5037 (ttm) REVERT: D 398 ARG cc_start: 0.6752 (ttm170) cc_final: 0.6292 (ttm170) REVERT: E 45 ARG cc_start: 0.8986 (ptt90) cc_final: 0.8731 (ptm-80) REVERT: E 70 THR cc_start: 0.8721 (m) cc_final: 0.8431 (p) REVERT: E 72 MET cc_start: 0.8495 (tpp) cc_final: 0.8171 (tpp) REVERT: E 96 ASP cc_start: 0.8334 (m-30) cc_final: 0.7970 (m-30) REVERT: E 105 MET cc_start: 0.8097 (mmm) cc_final: 0.7412 (ptm) REVERT: E 113 ASP cc_start: 0.8740 (p0) cc_final: 0.8441 (p0) REVERT: E 130 ASP cc_start: 0.8391 (m-30) cc_final: 0.7996 (m-30) REVERT: E 138 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8561 (mtpp) REVERT: E 156 MET cc_start: 0.8230 (mmt) cc_final: 0.7589 (mmt) REVERT: E 292 LYS cc_start: 0.8430 (mttt) cc_final: 0.7990 (mttp) REVERT: E 295 TYR cc_start: 0.8275 (p90) cc_final: 0.7622 (p90) outliers start: 44 outliers final: 41 residues processed: 348 average time/residue: 0.2624 time to fit residues: 132.4356 Evaluate side-chains 358 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 315 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.2980 chunk 124 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 0.0070 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.184255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145745 restraints weight = 17900.171| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.41 r_work: 0.3403 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14585 Z= 0.138 Angle : 0.539 9.283 19775 Z= 0.261 Chirality : 0.042 0.143 2265 Planarity : 0.003 0.041 2450 Dihedral : 4.126 18.371 2200 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.39 % Allowed : 20.84 % Favored : 76.77 % 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: -0.68 (0.21), residues: 1710 helix: 0.35 (0.26), residues: 500 sheet: -0.61 (0.27), residues: 370 loop : -0.78 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 422 HIS 0.002 0.001 HIS A 231 PHE 0.013 0.001 PHE A 417 TYR 0.015 0.001 TYR C 317 ARG 0.008 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3509.67 seconds wall clock time: 64 minutes 12.55 seconds (3852.55 seconds total)