Starting phenix.real_space_refine on Tue Nov 19 15:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyq_34376/11_2024/8gyq_34376.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyq_34376/11_2024/8gyq_34376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyq_34376/11_2024/8gyq_34376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyq_34376/11_2024/8gyq_34376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyq_34376/11_2024/8gyq_34376.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyq_34376/11_2024/8gyq_34376.cif" } resolution = 3.4 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= 0.006 sd= 0.088 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 91 5.16 5 C 12726 2.51 5 N 3402 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "E" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "G" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.18, per 1000 atoms: 0.57 Number of scatterers: 19712 At special positions: 0 Unit cell: (125.19, 125.19, 127.33, 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 91 16.00 O 3493 8.00 N 3402 7.00 C 12726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 279 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 279 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 279 " distance=2.03 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 259 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 279 " distance=2.03 Simple disulfide: pdb=" SG CYS G 99 " - pdb=" SG CYS G 259 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 NAG-ASN " NAG A 701 " - " ASN A 86 " " NAG B 701 " - " ASN B 86 " " NAG C 701 " - " ASN C 86 " " NAG D 701 " - " ASN D 86 " " NAG E 701 " - " ASN E 86 " " NAG F 701 " - " ASN F 86 " " NAG G 701 " - " ASN G 86 " Time building additional restraints: 5.01 Conformation dependent library (CDL) restraints added in 2.4 seconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 75.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 48 through 76 removed outlier: 3.815A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.767A pdb=" N TRP A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 183 removed outlier: 4.011A pdb=" N LYS A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.291A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Proline residue: A 138 - end of helix removed outlier: 5.472A pdb=" N THR A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix removed outlier: 4.004A pdb=" N GLU A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.827A pdb=" N ARG A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 251 removed outlier: 3.836A pdb=" N VAL A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix removed outlier: 3.759A pdb=" N THR A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 314 removed outlier: 3.624A pdb=" N GLY A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 removed outlier: 3.783A pdb=" N VAL A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.589A pdb=" N TRP A 336 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.675A pdb=" N ILE A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 367 removed outlier: 3.897A pdb=" N ASN A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 4.262A pdb=" N ASP A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.699A pdb=" N ALA A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.502A pdb=" N ARG B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.900A pdb=" N TRP B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 183 removed outlier: 3.932A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.404A pdb=" N LEU B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 5.691A pdb=" N THR B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 4.023A pdb=" N GLU B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.928A pdb=" N ARG B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 251 removed outlier: 3.871A pdb=" N VAL B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 283 through 314 Processing helix chain 'B' and resid 319 through 329 removed outlier: 3.911A pdb=" N VAL B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.615A pdb=" N TRP B 336 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.634A pdb=" N ILE B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.919A pdb=" N ASN B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 removed outlier: 3.891A pdb=" N ASP B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.976A pdb=" N ALA B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 76 removed outlier: 3.862A pdb=" N ARG C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.943A pdb=" N TRP C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 183 removed outlier: 3.998A pdb=" N LYS C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Proline residue: C 125 - end of helix removed outlier: 4.349A pdb=" N LEU C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 5.666A pdb=" N THR C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Proline residue: C 174 - end of helix removed outlier: 4.048A pdb=" N GLU C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 251 removed outlier: 3.836A pdb=" N VAL C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Proline residue: C 241 - end of helix Processing helix chain 'C' and resid 283 through 314 removed outlier: 3.523A pdb=" N GLY C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.752A pdb=" N VAL C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.593A pdb=" N TRP C 336 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.929A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 358 through 367 removed outlier: 3.916A pdb=" N ASN C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.725A pdb=" N ASP C 376 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.710A pdb=" N ALA C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 76 removed outlier: 3.789A pdb=" N ARG D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Proline residue: D 62 - end of helix Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.888A pdb=" N TRP D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 183 removed outlier: 3.992A pdb=" N LYS D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Proline residue: D 125 - end of helix removed outlier: 4.316A pdb=" N LEU D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 5.734A pdb=" N THR D 148 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 159 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix removed outlier: 4.059A pdb=" N GLU D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 251 removed outlier: 3.848A pdb=" N VAL D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Proline residue: D 241 - end of helix removed outlier: 3.784A pdb=" N THR D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 314 removed outlier: 3.572A pdb=" N GLY D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.762A pdb=" N VAL D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.563A pdb=" N TRP D 336 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.907A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.801A pdb=" N ASN D 362 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 376 removed outlier: 4.019A pdb=" N ASP D 376 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 389 removed outlier: 3.717A pdb=" N ALA D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 76 removed outlier: 5.107A pdb=" N VAL E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.812A pdb=" N TRP E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 183 removed outlier: 4.001A pdb=" N LYS E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Proline residue: E 125 - end of helix removed outlier: 4.308A pdb=" N LEU E 129 " --> pdb=" O PRO E 125 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 5.663A pdb=" N THR E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Proline residue: E 174 - end of helix removed outlier: 4.030A pdb=" N GLU E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 202 Processing helix chain 'E' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 251 removed outlier: 3.842A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Proline residue: E 241 - end of helix removed outlier: 3.566A pdb=" N THR E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 314 removed outlier: 3.602A pdb=" N GLY E 292 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 removed outlier: 3.767A pdb=" N VAL E 328 " --> pdb=" O LYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.582A pdb=" N TRP E 336 " --> pdb=" O ARG E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 3.864A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 358 through 367 removed outlier: 3.888A pdb=" N ASN E 362 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG E 363 " --> pdb=" O LYS E 359 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 366 " --> pdb=" O ASN E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.954A pdb=" N ASP E 376 " --> pdb=" O LEU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.730A pdb=" N ALA E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 removed outlier: 5.112A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Proline residue: F 62 - end of helix Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.828A pdb=" N TRP F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 183 removed outlier: 4.028A pdb=" N LYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Proline residue: F 125 - end of helix removed outlier: 4.377A pdb=" N LEU F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Proline residue: F 138 - end of helix removed outlier: 5.491A pdb=" N THR F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Proline residue: F 174 - end of helix removed outlier: 4.015A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 204 through 219 removed outlier: 3.816A pdb=" N ARG F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 251 removed outlier: 3.843A pdb=" N VAL F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Proline residue: F 241 - end of helix removed outlier: 3.746A pdb=" N THR F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 314 removed outlier: 3.641A pdb=" N GLY F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 329 removed outlier: 3.783A pdb=" N VAL F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 removed outlier: 3.590A pdb=" N TRP F 336 " --> pdb=" O ARG F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.794A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'F' and resid 358 through 367 removed outlier: 4.045A pdb=" N ASN F 362 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 376 removed outlier: 4.190A pdb=" N ASP F 376 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.682A pdb=" N ALA F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 76 removed outlier: 5.109A pdb=" N VAL G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) Proline residue: G 62 - end of helix Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.810A pdb=" N TRP G 100 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 183 removed outlier: 3.964A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Proline residue: G 125 - end of helix removed outlier: 4.283A pdb=" N LEU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Proline residue: G 138 - end of helix removed outlier: 5.496A pdb=" N THR G 148 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARG G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN G 159 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) Proline residue: G 174 - end of helix removed outlier: 4.001A pdb=" N GLU G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'G' and resid 204 through 219 removed outlier: 3.846A pdb=" N ARG G 219 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 251 removed outlier: 3.854A pdb=" N VAL G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Proline residue: G 241 - end of helix Processing helix chain 'G' and resid 283 through 314 removed outlier: 3.578A pdb=" N GLY G 292 " --> pdb=" O ARG G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 removed outlier: 3.784A pdb=" N VAL G 328 " --> pdb=" O LYS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 removed outlier: 3.594A pdb=" N TRP G 336 " --> pdb=" O ARG G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.990A pdb=" N ILE G 346 " --> pdb=" O CYS G 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 358 through 367 removed outlier: 3.958A pdb=" N ASN G 362 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG G 363 " --> pdb=" O LYS G 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 366 " --> pdb=" O ASN G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 376 removed outlier: 4.260A pdb=" N ASP G 376 " --> pdb=" O LEU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.691A pdb=" N ALA G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 1244 hydrogen bonds defined for protein. 3669 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: 5.69 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6310 1.34 - 1.46: 2516 1.46 - 1.57: 11186 1.57 - 1.69: 1 1.69 - 1.81: 119 Bond restraints: 20132 Sorted by residual: bond pdb=" CG PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 1.503 1.416 0.087 3.40e-02 8.65e+02 6.48e+00 bond pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.10e+00 bond pdb=" N LEU D 48 " pdb=" CA LEU D 48 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.41e-02 5.03e+03 5.00e+00 bond pdb=" CB PRO C 49 " pdb=" CG PRO C 49 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" C PRO A 49 " pdb=" O PRO A 49 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.30e-02 5.92e+03 1.69e+00 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26746 1.79 - 3.58: 456 3.58 - 5.37: 60 5.37 - 7.16: 4 7.16 - 8.95: 6 Bond angle restraints: 27272 Sorted by residual: angle pdb=" CA PRO C 49 " pdb=" N PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 112.00 103.61 8.39 1.40e+00 5.10e-01 3.59e+01 angle pdb=" N PRO C 49 " pdb=" CD PRO C 49 " pdb=" CG PRO C 49 " ideal model delta sigma weight residual 103.20 96.31 6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" CB LYS A 203 " pdb=" CG LYS A 203 " pdb=" CD LYS A 203 " ideal model delta sigma weight residual 111.30 120.25 -8.95 2.30e+00 1.89e-01 1.51e+01 angle pdb=" CB LYS F 203 " pdb=" CG LYS F 203 " pdb=" CD LYS F 203 " ideal model delta sigma weight residual 111.30 118.99 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" CB LYS C 203 " pdb=" CG LYS C 203 " pdb=" CD LYS C 203 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 ... (remaining 27267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10459 17.93 - 35.87: 1345 35.87 - 53.80: 430 53.80 - 71.73: 57 71.73 - 89.67: 22 Dihedral angle restraints: 12313 sinusoidal: 5138 harmonic: 7175 Sorted by residual: dihedral pdb=" CA VAL A 378 " pdb=" C VAL A 378 " pdb=" N VAL A 379 " pdb=" CA VAL A 379 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA VAL G 378 " pdb=" C VAL G 378 " pdb=" N VAL G 379 " pdb=" CA VAL G 379 " ideal model delta harmonic sigma weight residual -180.00 -157.05 -22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA VAL D 378 " pdb=" C VAL D 378 " pdb=" N VAL D 379 " pdb=" CA VAL D 379 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 12310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2228 0.033 - 0.067: 660 0.067 - 0.100: 174 0.100 - 0.133: 58 0.133 - 0.167: 2 Chirality restraints: 3122 Sorted by residual: chirality pdb=" CA LEU A 48 " pdb=" N LEU A 48 " pdb=" C LEU A 48 " pdb=" CB LEU A 48 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA LEU D 48 " pdb=" N LEU D 48 " pdb=" C LEU D 48 " pdb=" CB LEU D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA PRO B 49 " pdb=" N PRO B 49 " pdb=" C PRO B 49 " pdb=" CB PRO B 49 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 3119 not shown) Planarity restraints: 3465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 86 " -0.167 2.00e-02 2.50e+03 3.18e-01 1.27e+03 pdb=" CG ASN C 86 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN C 86 " -0.121 2.00e-02 2.50e+03 pdb=" ND2 ASN C 86 " 0.565 2.00e-02 2.50e+03 pdb=" C1 NAG C 701 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 86 " -0.189 2.00e-02 2.50e+03 2.25e-01 6.34e+02 pdb=" CG ASN B 86 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 86 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 86 " 0.374 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.269 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 86 " 0.083 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN G 86 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN G 86 " 0.074 2.00e-02 2.50e+03 pdb=" ND2 ASN G 86 " -0.289 2.00e-02 2.50e+03 pdb=" C1 NAG G 701 " 0.176 2.00e-02 2.50e+03 ... (remaining 3462 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 114 2.45 - 3.06: 14039 3.06 - 3.68: 30523 3.68 - 4.29: 41389 4.29 - 4.90: 69771 Nonbonded interactions: 155836 Sorted by model distance: nonbonded pdb=" OD2 ASP C 51 " pdb=" OH TYR C 227 " model vdw 1.840 3.040 nonbonded pdb=" OG1 THR D 88 " pdb=" OD1 ASP D 90 " model vdw 1.903 3.040 nonbonded pdb=" OD2 ASP A 51 " pdb=" OH TYR A 227 " model vdw 1.914 3.040 nonbonded pdb=" OG1 THR B 88 " pdb=" OD1 ASP B 90 " model vdw 1.956 3.040 nonbonded pdb=" OD2 ASP F 51 " pdb=" OH TYR F 227 " model vdw 2.003 3.040 ... (remaining 155831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.680 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.590 Find NCS groups from input model: 0.870 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: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20132 Z= 0.196 Angle : 0.581 8.952 27272 Z= 0.306 Chirality : 0.035 0.167 3122 Planarity : 0.005 0.149 3458 Dihedral : 17.626 89.668 7595 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.27 % Favored : 92.56 % Rotamer: Outliers : 0.66 % Allowed : 26.32 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2394 helix: 1.49 (0.13), residues: 1540 sheet: -1.76 (0.60), residues: 105 loop : -2.51 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.002 0.000 HIS D 357 PHE 0.019 0.001 PHE A 50 TYR 0.013 0.001 TYR B 249 ARG 0.005 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 HIS cc_start: 0.8494 (t70) cc_final: 0.7908 (t-170) REVERT: A 380 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7103 (mtt180) REVERT: C 160 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: C 342 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7970 (p) REVERT: D 326 HIS cc_start: 0.8307 (t70) cc_final: 0.7924 (t70) REVERT: D 342 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8149 (p) REVERT: D 350 PHE cc_start: 0.7413 (m-80) cc_final: 0.7158 (m-80) REVERT: E 160 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5686 (tt0) REVERT: E 326 HIS cc_start: 0.8445 (t70) cc_final: 0.8064 (t-170) REVERT: E 342 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7516 (p) REVERT: F 160 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5471 (tt0) REVERT: G 160 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.5309 (tt0) REVERT: G 326 HIS cc_start: 0.8651 (t70) cc_final: 0.8034 (t-170) REVERT: G 342 CYS cc_start: 0.8394 (t) cc_final: 0.7833 (p) REVERT: G 380 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6954 (mtt90) outliers start: 14 outliers final: 4 residues processed: 270 average time/residue: 0.2787 time to fit residues: 120.4938 Evaluate side-chains 240 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 365 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 0.0020 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 319 ASN B 163 ASN B 254 GLN B 326 HIS C 121 HIS C 319 ASN D 252 GLN D 254 GLN D 357 HIS F 207 GLN F 319 ASN G 254 GLN G 319 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20132 Z= 0.229 Angle : 0.658 11.663 27272 Z= 0.327 Chirality : 0.044 0.702 3122 Planarity : 0.005 0.094 3458 Dihedral : 7.176 77.409 2830 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.56 % Allowed : 24.20 % Favored : 71.24 % 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: 0.34 (0.19), residues: 2394 helix: 1.46 (0.13), residues: 1603 sheet: -1.66 (0.60), residues: 105 loop : -2.55 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 115 HIS 0.003 0.000 HIS D 357 PHE 0.024 0.001 PHE A 350 TYR 0.013 0.001 TYR A 165 ARG 0.013 0.000 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 249 time to evaluate : 2.400 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7105 (tp) cc_final: 0.6857 (tp) REVERT: A 160 GLU cc_start: 0.5015 (OUTLIER) cc_final: 0.4223 (tt0) REVERT: A 210 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: A 326 HIS cc_start: 0.8490 (t70) cc_final: 0.7888 (t-170) REVERT: B 51 ASP cc_start: 0.7199 (m-30) cc_final: 0.6958 (m-30) REVERT: B 252 GLN cc_start: 0.8006 (tp40) cc_final: 0.7734 (tp40) REVERT: B 374 MET cc_start: 0.7664 (pmm) cc_final: 0.7431 (pmm) REVERT: C 135 MET cc_start: 0.8788 (tpp) cc_final: 0.8554 (mmm) REVERT: C 160 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.5535 (tt0) REVERT: C 210 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: D 191 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7350 (tm-30) REVERT: D 210 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: D 326 HIS cc_start: 0.8256 (t70) cc_final: 0.7971 (t70) REVERT: D 350 PHE cc_start: 0.7571 (m-80) cc_final: 0.7202 (m-80) REVERT: E 160 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5224 (tt0) REVERT: E 207 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: E 210 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: E 326 HIS cc_start: 0.8476 (t70) cc_final: 0.8069 (t-170) REVERT: F 160 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.4840 (tt0) REVERT: F 210 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: G 160 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.5203 (tt0) REVERT: G 326 HIS cc_start: 0.8645 (t70) cc_final: 0.8046 (t-170) REVERT: G 342 CYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7765 (p) outliers start: 97 outliers final: 52 residues processed: 309 average time/residue: 0.2829 time to fit residues: 141.0619 Evaluate side-chains 274 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 207 GLN Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 179 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 216 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 192 optimal weight: 0.5980 chunk 214 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS C 319 ASN C 362 ASN E 254 GLN F 121 HIS F 319 ASN F 362 ASN G 319 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20132 Z= 0.203 Angle : 0.616 10.820 27272 Z= 0.306 Chirality : 0.042 0.598 3122 Planarity : 0.005 0.073 3458 Dihedral : 6.690 70.892 2819 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.93 % Allowed : 24.86 % Favored : 70.21 % 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: 0.55 (0.18), residues: 2394 helix: 1.62 (0.13), residues: 1624 sheet: -1.51 (0.59), residues: 105 loop : -2.58 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.004 0.001 HIS B 326 PHE 0.026 0.001 PHE F 350 TYR 0.019 0.001 TYR B 213 ARG 0.006 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 233 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7241 (tp) cc_final: 0.6992 (tp) REVERT: A 160 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.4188 (tt0) REVERT: A 210 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.5874 (m-80) REVERT: A 326 HIS cc_start: 0.8542 (t70) cc_final: 0.7924 (t-170) REVERT: B 51 ASP cc_start: 0.7322 (m-30) cc_final: 0.7095 (m-30) REVERT: C 160 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5289 (tt0) REVERT: C 210 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: D 210 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: D 350 PHE cc_start: 0.7514 (m-80) cc_final: 0.7162 (m-80) REVERT: E 160 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5194 (tt0) REVERT: E 210 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: E 326 HIS cc_start: 0.8439 (t70) cc_final: 0.8021 (t-170) REVERT: F 150 LEU cc_start: 0.6901 (tp) cc_final: 0.6579 (tp) REVERT: F 160 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.4978 (tt0) REVERT: F 210 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.5842 (m-80) REVERT: F 380 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7202 (mtt90) REVERT: G 42 LEU cc_start: 0.1302 (OUTLIER) cc_final: 0.1040 (pp) REVERT: G 160 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.4810 (tt0) REVERT: G 210 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: G 326 HIS cc_start: 0.8601 (t70) cc_final: 0.8018 (t-170) REVERT: G 342 CYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7785 (p) REVERT: G 350 PHE cc_start: 0.7487 (m-80) cc_final: 0.7222 (m-80) outliers start: 105 outliers final: 69 residues processed: 307 average time/residue: 0.2791 time to fit residues: 138.3547 Evaluate side-chains 292 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 0.0060 chunk 217 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN B 326 HIS B 362 ASN B 377 ASN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20132 Z= 0.186 Angle : 0.594 10.828 27272 Z= 0.296 Chirality : 0.041 0.545 3122 Planarity : 0.005 0.067 3458 Dihedral : 6.392 66.420 2819 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.26 % Allowed : 25.23 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2394 helix: 1.73 (0.13), residues: 1624 sheet: -1.39 (0.58), residues: 105 loop : -2.55 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.003 0.000 HIS B 326 PHE 0.041 0.001 PHE E 350 TYR 0.017 0.001 TYR B 213 ARG 0.004 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 224 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4933 (OUTLIER) cc_final: 0.4161 (tt0) REVERT: A 210 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.5854 (m-80) REVERT: A 326 HIS cc_start: 0.8553 (t70) cc_final: 0.8295 (t70) REVERT: A 380 ARG cc_start: 0.7548 (mtt180) cc_final: 0.7291 (mtm180) REVERT: B 51 ASP cc_start: 0.7371 (m-30) cc_final: 0.7136 (m-30) REVERT: B 191 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6541 (tp30) REVERT: B 377 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6399 (m-40) REVERT: C 160 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5268 (tt0) REVERT: C 191 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 210 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: C 380 ARG cc_start: 0.6631 (mtt180) cc_final: 0.6125 (mtm180) REVERT: D 135 MET cc_start: 0.8744 (tpp) cc_final: 0.8469 (mmm) REVERT: D 191 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 210 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.5908 (m-80) REVERT: D 350 PHE cc_start: 0.7511 (m-80) cc_final: 0.7151 (m-80) REVERT: E 160 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5170 (tt0) REVERT: E 210 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6119 (m-80) REVERT: E 326 HIS cc_start: 0.8485 (t70) cc_final: 0.8055 (t-170) REVERT: F 150 LEU cc_start: 0.7058 (tp) cc_final: 0.6768 (tp) REVERT: F 160 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.4956 (tt0) REVERT: F 210 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5878 (m-80) REVERT: F 380 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7467 (mtt90) REVERT: G 42 LEU cc_start: 0.1340 (OUTLIER) cc_final: 0.1103 (pp) REVERT: G 160 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.4757 (tt0) REVERT: G 210 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6166 (m-80) REVERT: G 326 HIS cc_start: 0.8619 (t70) cc_final: 0.8086 (t-170) REVERT: G 342 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7784 (p) REVERT: G 358 ILE cc_start: 0.5104 (OUTLIER) cc_final: 0.4900 (pt) REVERT: G 380 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7475 (mtm180) outliers start: 112 outliers final: 72 residues processed: 309 average time/residue: 0.2823 time to fit residues: 139.9949 Evaluate side-chains 289 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 201 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20132 Z= 0.245 Angle : 0.609 10.718 27272 Z= 0.304 Chirality : 0.041 0.539 3122 Planarity : 0.005 0.064 3458 Dihedral : 6.248 58.990 2819 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.72 % Allowed : 24.58 % Favored : 68.70 % 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: 0.66 (0.18), residues: 2394 helix: 1.69 (0.13), residues: 1638 sheet: -1.45 (0.57), residues: 105 loop : -2.61 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.003 0.001 HIS D 357 PHE 0.017 0.001 PHE A 350 TYR 0.016 0.001 TYR B 213 ARG 0.003 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 210 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.5007 (OUTLIER) cc_final: 0.4262 (tt0) REVERT: A 210 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.5836 (m-80) REVERT: A 326 HIS cc_start: 0.8601 (t70) cc_final: 0.8364 (t70) REVERT: A 358 ILE cc_start: 0.5371 (OUTLIER) cc_final: 0.5167 (pt) REVERT: B 51 ASP cc_start: 0.7547 (m-30) cc_final: 0.7260 (m-30) REVERT: B 191 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6650 (tp30) REVERT: C 160 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5933 (tt0) REVERT: C 191 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 210 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: D 135 MET cc_start: 0.8836 (tpp) cc_final: 0.8575 (mmm) REVERT: D 210 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: D 350 PHE cc_start: 0.7546 (m-80) cc_final: 0.7182 (m-80) REVERT: E 160 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5209 (tt0) REVERT: E 210 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: E 326 HIS cc_start: 0.8494 (t70) cc_final: 0.8084 (t-170) REVERT: F 150 LEU cc_start: 0.7320 (tp) cc_final: 0.7058 (tp) REVERT: F 160 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.4949 (tt0) REVERT: F 210 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.5966 (m-80) REVERT: F 380 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7534 (mtt90) REVERT: G 42 LEU cc_start: 0.1385 (OUTLIER) cc_final: 0.1139 (pp) REVERT: G 160 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.4759 (tt0) REVERT: G 210 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: G 326 HIS cc_start: 0.8631 (t70) cc_final: 0.8192 (t-170) REVERT: G 380 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7251 (mtm180) outliers start: 143 outliers final: 103 residues processed: 313 average time/residue: 0.2797 time to fit residues: 142.2791 Evaluate side-chains 314 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 197 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.0870 chunk 207 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 287 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 377 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20132 Z= 0.207 Angle : 0.596 8.938 27272 Z= 0.296 Chirality : 0.040 0.495 3122 Planarity : 0.005 0.069 3458 Dihedral : 5.989 58.458 2819 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.97 % Allowed : 26.08 % Favored : 67.95 % 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: 0.76 (0.18), residues: 2394 helix: 1.77 (0.13), residues: 1638 sheet: -1.32 (0.57), residues: 105 loop : -2.61 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 115 HIS 0.002 0.000 HIS A 311 PHE 0.026 0.001 PHE G 350 TYR 0.014 0.001 TYR B 213 ARG 0.004 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 226 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.7978 (mmp) cc_final: 0.7218 (mmt) REVERT: A 160 GLU cc_start: 0.4992 (OUTLIER) cc_final: 0.4252 (tt0) REVERT: A 210 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: A 326 HIS cc_start: 0.8584 (t70) cc_final: 0.8346 (t70) REVERT: B 51 ASP cc_start: 0.7540 (m-30) cc_final: 0.7241 (m-30) REVERT: B 191 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6697 (tp30) REVERT: B 210 PHE cc_start: 0.8333 (t80) cc_final: 0.7818 (t80) REVERT: C 160 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5929 (tt0) REVERT: C 210 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: D 135 MET cc_start: 0.8800 (tpp) cc_final: 0.8560 (mmm) REVERT: D 191 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7316 (tm-30) REVERT: D 210 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: D 350 PHE cc_start: 0.7519 (m-80) cc_final: 0.7171 (m-80) REVERT: E 160 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.4986 (tt0) REVERT: E 210 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: E 326 HIS cc_start: 0.8474 (t70) cc_final: 0.8084 (t-170) REVERT: E 342 CYS cc_start: 0.8231 (t) cc_final: 0.7622 (p) REVERT: F 150 LEU cc_start: 0.7269 (tp) cc_final: 0.7041 (tp) REVERT: F 160 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.4919 (tt0) REVERT: F 210 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6025 (m-80) REVERT: G 42 LEU cc_start: 0.1253 (OUTLIER) cc_final: 0.1033 (pp) REVERT: G 160 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.4909 (tt0) REVERT: G 210 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: G 326 HIS cc_start: 0.8634 (t70) cc_final: 0.8218 (t-170) REVERT: G 358 ILE cc_start: 0.4928 (OUTLIER) cc_final: 0.4721 (pt) REVERT: G 380 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7164 (mtm180) outliers start: 127 outliers final: 91 residues processed: 322 average time/residue: 0.2698 time to fit residues: 140.8771 Evaluate side-chains 306 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 201 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN B 198 ASN B 287 GLN D 207 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20132 Z= 0.196 Angle : 0.598 9.776 27272 Z= 0.299 Chirality : 0.040 0.499 3122 Planarity : 0.005 0.067 3458 Dihedral : 5.861 57.574 2819 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.02 % Allowed : 26.83 % Favored : 67.15 % 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: 0.81 (0.18), residues: 2394 helix: 1.82 (0.13), residues: 1631 sheet: -1.20 (0.57), residues: 105 loop : -2.59 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 115 HIS 0.002 0.000 HIS D 357 PHE 0.030 0.001 PHE F 350 TYR 0.015 0.001 TYR B 213 ARG 0.007 0.000 ARG E 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 224 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4431 (tt0) REVERT: A 210 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.5809 (m-80) REVERT: A 326 HIS cc_start: 0.8591 (t70) cc_final: 0.8343 (t70) REVERT: A 332 THR cc_start: 0.4379 (OUTLIER) cc_final: 0.4066 (p) REVERT: B 51 ASP cc_start: 0.7651 (m-30) cc_final: 0.7314 (m-30) REVERT: B 191 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6748 (tp30) REVERT: B 210 PHE cc_start: 0.8321 (t80) cc_final: 0.7927 (t80) REVERT: C 160 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: C 191 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 210 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: C 342 CYS cc_start: 0.8417 (t) cc_final: 0.7585 (p) REVERT: D 135 MET cc_start: 0.8755 (tpp) cc_final: 0.8531 (mmm) REVERT: D 191 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 210 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: D 350 PHE cc_start: 0.7477 (m-80) cc_final: 0.7118 (m-80) REVERT: E 160 GLU cc_start: 0.5661 (OUTLIER) cc_final: 0.4924 (tt0) REVERT: E 210 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: E 326 HIS cc_start: 0.8486 (t70) cc_final: 0.8081 (t-170) REVERT: E 342 CYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7478 (p) REVERT: F 160 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.4893 (tt0) REVERT: F 210 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: F 342 CYS cc_start: 0.8210 (t) cc_final: 0.7544 (p) REVERT: F 380 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7331 (mtt90) REVERT: G 42 LEU cc_start: 0.1258 (OUTLIER) cc_final: 0.1039 (pp) REVERT: G 160 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.4849 (tt0) REVERT: G 210 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: G 326 HIS cc_start: 0.8637 (t70) cc_final: 0.8213 (t-170) REVERT: G 342 CYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7639 (p) REVERT: G 358 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4993 (pt) REVERT: G 380 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7181 (mtm180) outliers start: 128 outliers final: 90 residues processed: 319 average time/residue: 0.2910 time to fit residues: 147.7211 Evaluate side-chains 312 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 205 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 0.0000 chunk 137 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 21 optimal weight: 0.0870 chunk 180 optimal weight: 5.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 254 GLN B 287 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20132 Z= 0.172 Angle : 0.600 9.493 27272 Z= 0.299 Chirality : 0.040 0.470 3122 Planarity : 0.005 0.064 3458 Dihedral : 5.669 56.613 2819 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.51 % Allowed : 28.81 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2394 helix: 1.88 (0.13), residues: 1645 sheet: -0.88 (0.58), residues: 105 loop : -2.58 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 115 HIS 0.002 0.000 HIS A 311 PHE 0.037 0.001 PHE G 350 TYR 0.025 0.001 TYR B 136 ARG 0.007 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 226 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.5093 (OUTLIER) cc_final: 0.4447 (tt0) REVERT: A 210 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.5802 (m-80) REVERT: A 326 HIS cc_start: 0.8562 (t70) cc_final: 0.8310 (t70) REVERT: A 332 THR cc_start: 0.4835 (OUTLIER) cc_final: 0.4512 (p) REVERT: B 51 ASP cc_start: 0.7612 (m-30) cc_final: 0.7320 (m-30) REVERT: B 210 PHE cc_start: 0.8353 (t80) cc_final: 0.7991 (t80) REVERT: C 160 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5871 (tt0) REVERT: C 191 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7650 (tm-30) REVERT: C 210 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: C 342 CYS cc_start: 0.8430 (t) cc_final: 0.7533 (p) REVERT: D 191 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7214 (tm-30) REVERT: D 210 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: D 342 CYS cc_start: 0.8342 (t) cc_final: 0.7820 (p) REVERT: D 350 PHE cc_start: 0.7493 (m-80) cc_final: 0.7125 (m-80) REVERT: E 160 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5127 (tt0) REVERT: E 210 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: E 326 HIS cc_start: 0.8489 (t70) cc_final: 0.8077 (t-170) REVERT: E 342 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7535 (p) REVERT: F 160 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5111 (tt0) REVERT: F 210 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.5855 (m-80) REVERT: F 326 HIS cc_start: 0.8491 (t70) cc_final: 0.8048 (t-170) REVERT: F 342 CYS cc_start: 0.8186 (t) cc_final: 0.7543 (p) REVERT: F 380 ARG cc_start: 0.7636 (mtt180) cc_final: 0.7212 (mtt90) REVERT: G 42 LEU cc_start: 0.1321 (OUTLIER) cc_final: 0.1091 (pp) REVERT: G 160 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.4787 (tt0) REVERT: G 210 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: G 326 HIS cc_start: 0.8637 (t70) cc_final: 0.8240 (t-170) REVERT: G 342 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7664 (p) REVERT: G 358 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.5061 (pt) outliers start: 96 outliers final: 69 residues processed: 295 average time/residue: 0.2886 time to fit residues: 135.1826 Evaluate side-chains 295 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20132 Z= 0.250 Angle : 0.630 8.444 27272 Z= 0.315 Chirality : 0.041 0.485 3122 Planarity : 0.005 0.068 3458 Dihedral : 5.761 58.144 2819 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.17 % Allowed : 28.10 % Favored : 66.73 % 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: 0.89 (0.18), residues: 2394 helix: 1.87 (0.13), residues: 1631 sheet: -1.08 (0.57), residues: 105 loop : -2.55 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 115 HIS 0.002 0.000 HIS D 357 PHE 0.032 0.001 PHE F 350 TYR 0.019 0.001 TYR B 213 ARG 0.006 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 222 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.4602 (tt0) REVERT: A 210 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.5815 (m-80) REVERT: A 326 HIS cc_start: 0.8661 (t70) cc_final: 0.8404 (t70) REVERT: A 332 THR cc_start: 0.4928 (OUTLIER) cc_final: 0.4615 (p) REVERT: A 380 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7096 (mtm-85) REVERT: B 51 ASP cc_start: 0.7709 (m-30) cc_final: 0.7373 (m-30) REVERT: B 135 MET cc_start: 0.8840 (mmm) cc_final: 0.8454 (mmm) REVERT: B 190 ARG cc_start: 0.7865 (tmm160) cc_final: 0.6506 (mtm180) REVERT: B 191 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: B 210 PHE cc_start: 0.8417 (t80) cc_final: 0.8172 (t80) REVERT: C 160 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5914 (tt0) REVERT: C 191 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 210 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: C 342 CYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7676 (p) REVERT: D 191 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7198 (tm-30) REVERT: D 210 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: D 350 PHE cc_start: 0.7506 (m-80) cc_final: 0.7145 (m-80) REVERT: E 160 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5156 (tt0) REVERT: E 210 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: E 326 HIS cc_start: 0.8515 (t70) cc_final: 0.8069 (t-170) REVERT: E 342 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7450 (p) REVERT: F 160 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5141 (tt0) REVERT: F 210 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6062 (m-80) REVERT: F 326 HIS cc_start: 0.8500 (t70) cc_final: 0.8093 (t-170) REVERT: G 42 LEU cc_start: 0.1297 (OUTLIER) cc_final: 0.1066 (pp) REVERT: G 135 MET cc_start: 0.8622 (mmm) cc_final: 0.8361 (mmm) REVERT: G 160 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.4736 (tt0) REVERT: G 210 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6205 (m-80) REVERT: G 326 HIS cc_start: 0.8665 (t70) cc_final: 0.8299 (t-170) REVERT: G 358 ILE cc_start: 0.5327 (OUTLIER) cc_final: 0.5069 (pt) outliers start: 110 outliers final: 84 residues processed: 302 average time/residue: 0.3013 time to fit residues: 142.8965 Evaluate side-chains 314 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 213 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 GLN B 287 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20132 Z= 0.178 Angle : 0.610 9.344 27272 Z= 0.304 Chirality : 0.040 0.455 3122 Planarity : 0.005 0.063 3458 Dihedral : 5.591 57.081 2819 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.09 % Allowed : 29.14 % Favored : 66.78 % 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: 1.02 (0.18), residues: 2394 helix: 1.90 (0.13), residues: 1645 sheet: -0.85 (0.59), residues: 105 loop : -2.45 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 115 HIS 0.002 0.000 HIS F 311 PHE 0.017 0.001 PHE B 350 TYR 0.017 0.001 TYR B 213 ARG 0.007 0.000 ARG G 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 224 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.5081 (OUTLIER) cc_final: 0.4466 (tt0) REVERT: A 210 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.5775 (m-80) REVERT: A 326 HIS cc_start: 0.8622 (t70) cc_final: 0.8366 (t70) REVERT: A 332 THR cc_start: 0.4725 (OUTLIER) cc_final: 0.4387 (p) REVERT: A 349 MET cc_start: 0.7690 (mtp) cc_final: 0.7458 (mtp) REVERT: B 51 ASP cc_start: 0.7672 (m-30) cc_final: 0.7352 (m-30) REVERT: B 190 ARG cc_start: 0.8031 (tmm160) cc_final: 0.6663 (mtm180) REVERT: B 191 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7002 (tp30) REVERT: B 210 PHE cc_start: 0.8347 (t80) cc_final: 0.8089 (t80) REVERT: C 160 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5930 (tt0) REVERT: C 191 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 210 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: C 342 CYS cc_start: 0.8436 (t) cc_final: 0.7609 (p) REVERT: D 191 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7156 (tm-30) REVERT: D 210 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: D 342 CYS cc_start: 0.8355 (t) cc_final: 0.7910 (p) REVERT: D 350 PHE cc_start: 0.7497 (m-80) cc_final: 0.7134 (m-80) REVERT: D 380 ARG cc_start: 0.6962 (mtt90) cc_final: 0.6283 (mtm180) REVERT: E 160 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5125 (tt0) REVERT: E 210 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: E 326 HIS cc_start: 0.8529 (t70) cc_final: 0.8275 (t-170) REVERT: E 342 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7533 (p) REVERT: F 160 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5050 (tt0) REVERT: F 210 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6019 (m-80) REVERT: F 326 HIS cc_start: 0.8510 (t70) cc_final: 0.8072 (t-170) REVERT: F 380 ARG cc_start: 0.7636 (mtt180) cc_final: 0.7360 (mtt180) REVERT: G 42 LEU cc_start: 0.1376 (OUTLIER) cc_final: 0.1140 (pp) REVERT: G 135 MET cc_start: 0.8623 (mmm) cc_final: 0.8381 (mmm) REVERT: G 160 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4699 (tt0) REVERT: G 210 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6172 (m-80) REVERT: G 326 HIS cc_start: 0.8650 (t70) cc_final: 0.8279 (t-170) REVERT: G 342 CYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7741 (p) REVERT: G 358 ILE cc_start: 0.5279 (OUTLIER) cc_final: 0.5029 (pt) REVERT: G 380 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7007 (mtm180) outliers start: 87 outliers final: 65 residues processed: 289 average time/residue: 0.3009 time to fit residues: 137.4947 Evaluate side-chains 297 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 215 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 79 optimal weight: 0.0050 chunk 194 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.198043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133533 restraints weight = 26991.755| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.66 r_work: 0.3538 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20132 Z= 0.178 Angle : 0.609 10.169 27272 Z= 0.304 Chirality : 0.040 0.446 3122 Planarity : 0.005 0.055 3458 Dihedral : 5.474 56.993 2819 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.28 % Allowed : 28.90 % Favored : 66.82 % 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: 1.05 (0.18), residues: 2394 helix: 1.93 (0.13), residues: 1645 sheet: -0.80 (0.60), residues: 105 loop : -2.45 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 115 HIS 0.002 0.000 HIS F 311 PHE 0.033 0.001 PHE F 350 TYR 0.016 0.001 TYR B 213 ARG 0.008 0.000 ARG A 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3858.51 seconds wall clock time: 71 minutes 26.51 seconds (4286.51 seconds total)