Starting phenix.real_space_refine on Sat Mar 16 08:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/03_2024/6ply_20380_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/03_2024/6ply_20380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/03_2024/6ply_20380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/03_2024/6ply_20380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/03_2024/6ply_20380_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/03_2024/6ply_20380_updated.pdb" } resolution = 2.9 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= 0.060 sd= 3.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9230 2.51 5 N 2275 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14165 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ABU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.58, per 1000 atoms: 0.54 Number of scatterers: 14165 At special positions: 0 Unit cell: (107.813, 104.521, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2560 8.00 N 2275 7.00 C 9230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 6.45 Conformation dependent library (CDL) restraints added in 2.6 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 25 sheets defined 31.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.537A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.685A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.950A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.531A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.858A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.815A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 427 removed outlier: 4.064A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.511A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.702A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.262A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 287 removed outlier: 3.770A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 323 removed outlier: 3.625A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.845A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 427 removed outlier: 4.089A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.545A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.721A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 245 through 254 removed outlier: 4.056A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 268 through 287 removed outlier: 3.854A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 308 through 323 removed outlier: 3.990A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.528A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 427 removed outlier: 4.016A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.568A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.680A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 239 through 242 No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 245 through 254 removed outlier: 3.975A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 268 through 287 removed outlier: 3.785A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 308 through 323 removed outlier: 3.840A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 No H-bonds generated for 'chain 'D' and resid 393 through 396' Processing helix chain 'D' and resid 401 through 404 No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 410 through 427 removed outlier: 4.052A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.600A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.716A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 245 through 258 removed outlier: 4.001A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 287 removed outlier: 3.826A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 No H-bonds generated for 'chain 'E' and resid 300 through 303' Processing helix chain 'E' and resid 306 through 323 removed outlier: 3.574A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 404 removed outlier: 3.540A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 427 removed outlier: 4.127A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.250A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.506A pdb=" N ILE A 226 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 211 through 213 Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.230A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= J, first strand: chain 'B' and resid 211 through 213 Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.217A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= M, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= O, first strand: chain 'C' and resid 211 through 213 Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.246A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'D' and resid 98 through 100 Processing sheet with id= S, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'D' and resid 211 through 213 Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.265A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= W, first strand: chain 'E' and resid 98 through 100 Processing sheet with id= X, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= Y, first strand: chain 'E' and resid 211 through 213 433 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 6.92 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: 4280 1.34 - 1.46: 3608 1.46 - 1.58: 6452 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 14510 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 14505 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 389 106.04 - 113.05: 7717 113.05 - 120.06: 5274 120.06 - 127.06: 6111 127.06 - 134.07: 189 Bond angle restraints: 19680 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.58 -11.04 1.91e+00 2.74e-01 3.34e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.56 -11.02 1.91e+00 2.74e-01 3.33e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" N VAL E 37 " pdb=" CA VAL E 37 " pdb=" C VAL E 37 " ideal model delta sigma weight residual 113.71 108.92 4.79 9.50e-01 1.11e+00 2.54e+01 ... (remaining 19675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 8413 16.54 - 33.07: 350 33.07 - 49.61: 47 49.61 - 66.15: 36 66.15 - 82.69: 29 Dihedral angle restraints: 8875 sinusoidal: 3760 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual -180.00 -153.29 -26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 8872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1509 0.052 - 0.104: 588 0.104 - 0.156: 122 0.156 - 0.208: 29 0.208 - 0.260: 12 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.50e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 410 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO E 411 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 411 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 411 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO B 411 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO A 411 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.039 5.00e-02 4.00e+02 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4578 2.84 - 3.36: 12208 3.36 - 3.87: 22583 3.87 - 4.39: 26969 4.39 - 4.90: 45362 Nonbonded interactions: 111700 Sorted by model distance: nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.330 2.440 nonbonded pdb=" OE2 GLU A 69 " pdb=" NH2 ARG A 234 " model vdw 2.335 2.520 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.342 2.440 nonbonded pdb=" OE2 GLU D 69 " pdb=" NH2 ARG D 234 " model vdw 2.343 2.520 ... (remaining 111695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 428) selection = (chain 'B' and resid 23 through 428) selection = (chain 'C' and resid 23 through 428) selection = (chain 'D' and resid 23 through 428) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.330 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 40.740 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.007 0.057 14510 Z= 0.461 Angle : 1.026 11.234 19680 Z= 0.525 Chirality : 0.058 0.260 2260 Planarity : 0.007 0.073 2435 Dihedral : 11.636 82.687 5525 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.14), residues: 1710 helix: -4.84 (0.08), residues: 560 sheet: -2.43 (0.22), residues: 390 loop : -2.73 (0.17), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 110 HIS 0.004 0.001 HIS E 231 PHE 0.023 0.003 PHE D 115 TYR 0.028 0.003 TYR A 425 ARG 0.008 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 1.716 Fit side-chains REVERT: A 43 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8385 (mtm180) REVERT: A 97 ASP cc_start: 0.8116 (m-30) cc_final: 0.7368 (t0) REVERT: A 105 MET cc_start: 0.8044 (mmp) cc_final: 0.7742 (mmm) REVERT: A 126 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 138 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8281 (mttm) REVERT: A 181 ASP cc_start: 0.8159 (m-30) cc_final: 0.7919 (m-30) REVERT: A 206 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7600 (mttm) REVERT: A 210 ASP cc_start: 0.8100 (m-30) cc_final: 0.7516 (m-30) REVERT: A 227 GLU cc_start: 0.8340 (pt0) cc_final: 0.7980 (pt0) REVERT: A 233 GLU cc_start: 0.7087 (tt0) cc_final: 0.6725 (tt0) REVERT: A 420 PHE cc_start: 0.7620 (t80) cc_final: 0.7404 (t80) REVERT: B 28 GLU cc_start: 0.8571 (tp30) cc_final: 0.8354 (mt-10) REVERT: B 43 ARG cc_start: 0.9082 (mtm-85) cc_final: 0.8552 (mtm180) REVERT: B 75 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6928 (mtp-110) REVERT: B 93 GLU cc_start: 0.8698 (pp20) cc_final: 0.8461 (pp20) REVERT: B 97 ASP cc_start: 0.8178 (m-30) cc_final: 0.7471 (t0) REVERT: B 105 MET cc_start: 0.8038 (mmp) cc_final: 0.7798 (mmm) REVERT: B 113 ASP cc_start: 0.8407 (p0) cc_final: 0.7928 (p0) REVERT: B 126 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 138 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8354 (mttt) REVERT: B 227 GLU cc_start: 0.8427 (pt0) cc_final: 0.8072 (pt0) REVERT: B 246 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7547 (Cg_endo) REVERT: C 28 GLU cc_start: 0.8516 (tp30) cc_final: 0.8277 (tt0) REVERT: C 43 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8697 (mtp180) REVERT: C 75 ARG cc_start: 0.7232 (ttm-80) cc_final: 0.6889 (mtp-110) REVERT: C 97 ASP cc_start: 0.8055 (m-30) cc_final: 0.7483 (t0) REVERT: C 113 ASP cc_start: 0.8457 (p0) cc_final: 0.7925 (p0) REVERT: C 126 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7217 (mt-10) REVERT: C 130 ASP cc_start: 0.7824 (m-30) cc_final: 0.7568 (m-30) REVERT: C 181 ASP cc_start: 0.8116 (m-30) cc_final: 0.7738 (m-30) REVERT: C 206 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7485 (mttm) REVERT: C 210 ASP cc_start: 0.7964 (m-30) cc_final: 0.7649 (m-30) REVERT: C 227 GLU cc_start: 0.8276 (pt0) cc_final: 0.7934 (pt0) REVERT: C 246 PRO cc_start: 0.7945 (Cg_exo) cc_final: 0.7705 (Cg_endo) REVERT: D 27 SER cc_start: 0.7970 (t) cc_final: 0.7748 (t) REVERT: D 43 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8539 (mtm180) REVERT: D 72 MET cc_start: 0.8691 (mtm) cc_final: 0.8449 (mtt) REVERT: D 75 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6826 (mtp-110) REVERT: D 97 ASP cc_start: 0.8124 (m-30) cc_final: 0.7389 (t0) REVERT: D 126 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7255 (mt-10) REVERT: D 138 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8238 (mttm) REVERT: D 206 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7851 (mtmt) REVERT: D 210 ASP cc_start: 0.8085 (m-30) cc_final: 0.7691 (m-30) REVERT: D 303 MET cc_start: 0.9210 (mmm) cc_final: 0.8711 (mmt) REVERT: E 28 GLU cc_start: 0.8582 (tp30) cc_final: 0.8285 (tt0) REVERT: E 43 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.8590 (mtm180) REVERT: E 97 ASP cc_start: 0.7961 (m-30) cc_final: 0.7229 (t0) REVERT: E 126 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7134 (pm20) REVERT: E 210 ASP cc_start: 0.8079 (m-30) cc_final: 0.7573 (m-30) REVERT: E 227 GLU cc_start: 0.8355 (pt0) cc_final: 0.7978 (pt0) REVERT: E 233 GLU cc_start: 0.7081 (tt0) cc_final: 0.6783 (tt0) REVERT: E 246 PRO cc_start: 0.7798 (Cg_exo) cc_final: 0.7572 (Cg_endo) REVERT: E 419 ILE cc_start: 0.8102 (mt) cc_final: 0.7825 (mt) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 1.1472 time to fit residues: 569.6994 Evaluate side-chains 324 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN A 180 ASN B 62 ASN B 180 ASN B 231 HIS B 282 GLN C 62 ASN C 82 GLN C 282 GLN D 62 ASN D 123 ASN D 282 GLN E 62 ASN E 82 GLN E 180 ASN E 282 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14510 Z= 0.218 Angle : 0.687 6.817 19680 Z= 0.346 Chirality : 0.047 0.181 2260 Planarity : 0.005 0.044 2435 Dihedral : 9.836 52.143 2195 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.86 % Allowed : 13.79 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.16), residues: 1710 helix: -3.52 (0.14), residues: 565 sheet: -1.53 (0.26), residues: 345 loop : -2.55 (0.17), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 259 HIS 0.002 0.000 HIS B 231 PHE 0.016 0.002 PHE A 322 TYR 0.015 0.002 TYR A 317 ARG 0.004 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 337 time to evaluate : 1.633 Fit side-chains REVERT: A 43 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8667 (mtm180) REVERT: A 97 ASP cc_start: 0.8089 (m-30) cc_final: 0.7349 (t0) REVERT: A 126 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 130 ASP cc_start: 0.7946 (m-30) cc_final: 0.7452 (m-30) REVERT: A 138 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8241 (mttm) REVERT: A 181 ASP cc_start: 0.8124 (m-30) cc_final: 0.7902 (m-30) REVERT: A 206 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7522 (mttm) REVERT: A 210 ASP cc_start: 0.8038 (m-30) cc_final: 0.7620 (m-30) REVERT: A 227 GLU cc_start: 0.8037 (pt0) cc_final: 0.7799 (pt0) REVERT: A 391 MET cc_start: 0.5873 (tpt) cc_final: 0.5638 (tpt) REVERT: B 28 GLU cc_start: 0.8539 (tp30) cc_final: 0.8205 (tt0) REVERT: B 43 ARG cc_start: 0.9041 (mtm-85) cc_final: 0.8788 (mtm180) REVERT: B 75 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.6996 (mtp-110) REVERT: B 97 ASP cc_start: 0.8100 (m-30) cc_final: 0.7445 (t0) REVERT: B 113 ASP cc_start: 0.8414 (p0) cc_final: 0.7955 (p0) REVERT: B 126 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7258 (mt-10) REVERT: B 138 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8381 (mtpp) REVERT: B 235 GLN cc_start: 0.8158 (mm110) cc_final: 0.7719 (mt0) REVERT: B 418 ASN cc_start: 0.8070 (m-40) cc_final: 0.7657 (m-40) REVERT: B 423 ILE cc_start: 0.9102 (mt) cc_final: 0.8879 (mp) REVERT: C 28 GLU cc_start: 0.8499 (tp30) cc_final: 0.8228 (tt0) REVERT: C 72 MET cc_start: 0.8813 (mtt) cc_final: 0.8592 (mtt) REVERT: C 75 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.6942 (mtp-110) REVERT: C 97 ASP cc_start: 0.8051 (m-30) cc_final: 0.7465 (t0) REVERT: C 113 ASP cc_start: 0.8504 (p0) cc_final: 0.8027 (p0) REVERT: C 126 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7152 (mt-10) REVERT: C 130 ASP cc_start: 0.7729 (m-30) cc_final: 0.7465 (m-30) REVERT: C 181 ASP cc_start: 0.8064 (m-30) cc_final: 0.7749 (m-30) REVERT: C 206 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7570 (mttm) REVERT: C 210 ASP cc_start: 0.7967 (m-30) cc_final: 0.7673 (m-30) REVERT: C 243 MET cc_start: 0.7649 (tpp) cc_final: 0.7231 (mtt) REVERT: C 303 MET cc_start: 0.9273 (mmt) cc_final: 0.9060 (mmt) REVERT: D 28 GLU cc_start: 0.8666 (tp30) cc_final: 0.8334 (tt0) REVERT: D 72 MET cc_start: 0.8709 (mtm) cc_final: 0.8425 (mtt) REVERT: D 75 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.6997 (mtp-110) REVERT: D 97 ASP cc_start: 0.7970 (m-30) cc_final: 0.7276 (t0) REVERT: D 126 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7311 (mt-10) REVERT: D 130 ASP cc_start: 0.7881 (m-30) cc_final: 0.7500 (m-30) REVERT: D 138 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8161 (mttm) REVERT: D 206 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7891 (mtmt) REVERT: D 210 ASP cc_start: 0.8019 (m-30) cc_final: 0.7657 (m-30) REVERT: D 303 MET cc_start: 0.9248 (mmm) cc_final: 0.8849 (mmt) REVERT: D 419 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7079 (mt) REVERT: D 423 ILE cc_start: 0.9021 (mt) cc_final: 0.8817 (mm) REVERT: E 28 GLU cc_start: 0.8505 (tp30) cc_final: 0.8155 (tt0) REVERT: E 43 ARG cc_start: 0.8973 (mtm-85) cc_final: 0.8596 (mtm180) REVERT: E 97 ASP cc_start: 0.7951 (m-30) cc_final: 0.7236 (t0) REVERT: E 105 MET cc_start: 0.7989 (mmm) cc_final: 0.7768 (mmm) REVERT: E 126 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7334 (mt-10) REVERT: E 208 GLU cc_start: 0.8337 (tp30) cc_final: 0.8109 (tp30) REVERT: E 303 MET cc_start: 0.9250 (mmt) cc_final: 0.9049 (mmt) REVERT: E 322 PHE cc_start: 0.7756 (t80) cc_final: 0.7334 (t80) REVERT: E 391 MET cc_start: 0.5997 (tpt) cc_final: 0.5789 (tpt) outliers start: 59 outliers final: 15 residues processed: 368 average time/residue: 1.0740 time to fit residues: 438.8846 Evaluate side-chains 327 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 311 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 316 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 82 GLN B 141 ASN C 180 ASN D 82 GLN E 62 ASN E 231 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14510 Z= 0.273 Angle : 0.673 9.000 19680 Z= 0.337 Chirality : 0.047 0.154 2260 Planarity : 0.004 0.045 2435 Dihedral : 8.368 43.015 2195 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.25 % Allowed : 16.08 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.18), residues: 1710 helix: -2.60 (0.18), residues: 570 sheet: -0.95 (0.27), residues: 345 loop : -2.34 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 422 HIS 0.002 0.001 HIS E 231 PHE 0.015 0.002 PHE D 64 TYR 0.015 0.002 TYR A 317 ARG 0.005 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 327 time to evaluate : 1.718 Fit side-chains REVERT: A 43 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8653 (mtm180) REVERT: A 72 MET cc_start: 0.8728 (mtm) cc_final: 0.8298 (mtt) REVERT: A 97 ASP cc_start: 0.8110 (m-30) cc_final: 0.7430 (t0) REVERT: A 126 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7199 (mt-10) REVERT: A 138 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8195 (mttm) REVERT: A 181 ASP cc_start: 0.8226 (m-30) cc_final: 0.7990 (m-30) REVERT: A 206 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7999 (mttt) REVERT: A 210 ASP cc_start: 0.8027 (m-30) cc_final: 0.7543 (m-30) REVERT: A 227 GLU cc_start: 0.8003 (pt0) cc_final: 0.7759 (pt0) REVERT: A 419 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7137 (mp) REVERT: A 423 ILE cc_start: 0.8983 (mt) cc_final: 0.8770 (mp) REVERT: B 28 GLU cc_start: 0.8554 (tp30) cc_final: 0.8207 (tt0) REVERT: B 96 ASP cc_start: 0.8579 (m-30) cc_final: 0.8079 (m-30) REVERT: B 97 ASP cc_start: 0.8118 (m-30) cc_final: 0.7542 (t0) REVERT: B 113 ASP cc_start: 0.8471 (p0) cc_final: 0.8038 (p0) REVERT: B 126 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 160 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.6998 (p0) REVERT: B 229 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7902 (mtp85) REVERT: B 235 GLN cc_start: 0.8190 (mm110) cc_final: 0.7789 (mt0) REVERT: B 243 MET cc_start: 0.7971 (tpp) cc_final: 0.7706 (mtt) REVERT: B 419 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7409 (mp) REVERT: B 420 PHE cc_start: 0.8348 (t80) cc_final: 0.7932 (m-80) REVERT: C 28 GLU cc_start: 0.8502 (tp30) cc_final: 0.8216 (tt0) REVERT: C 31 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: C 72 MET cc_start: 0.8842 (mtt) cc_final: 0.8610 (mtt) REVERT: C 97 ASP cc_start: 0.8054 (m-30) cc_final: 0.7511 (t0) REVERT: C 113 ASP cc_start: 0.8509 (p0) cc_final: 0.8066 (p0) REVERT: C 126 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7207 (mt-10) REVERT: C 130 ASP cc_start: 0.7794 (m-30) cc_final: 0.7534 (m-30) REVERT: C 181 ASP cc_start: 0.8171 (m-30) cc_final: 0.7851 (m-30) REVERT: C 206 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7761 (mttm) REVERT: C 210 ASP cc_start: 0.7963 (m-30) cc_final: 0.7681 (m-30) REVERT: C 227 GLU cc_start: 0.8369 (pt0) cc_final: 0.8006 (pt0) REVERT: C 243 MET cc_start: 0.7633 (tpp) cc_final: 0.7211 (mtt) REVERT: C 303 MET cc_start: 0.9298 (mmt) cc_final: 0.9061 (mmt) REVERT: C 398 ARG cc_start: 0.6941 (mtt90) cc_final: 0.6392 (tpt170) REVERT: C 419 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7467 (mt) REVERT: D 28 GLU cc_start: 0.8732 (tp30) cc_final: 0.8318 (tt0) REVERT: D 72 MET cc_start: 0.8783 (mtm) cc_final: 0.8568 (mtt) REVERT: D 75 ARG cc_start: 0.7386 (ttm-80) cc_final: 0.7087 (mtp-110) REVERT: D 97 ASP cc_start: 0.8095 (m-30) cc_final: 0.7419 (t0) REVERT: D 126 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7279 (mt-10) REVERT: D 206 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7650 (mttm) REVERT: D 210 ASP cc_start: 0.7994 (m-30) cc_final: 0.7635 (m-30) REVERT: D 303 MET cc_start: 0.9267 (mmm) cc_final: 0.8949 (mmt) REVERT: D 419 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7346 (mp) REVERT: D 420 PHE cc_start: 0.7844 (t80) cc_final: 0.7531 (t80) REVERT: E 28 GLU cc_start: 0.8558 (tp30) cc_final: 0.8210 (tt0) REVERT: E 43 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.8647 (mtm180) REVERT: E 97 ASP cc_start: 0.8060 (m-30) cc_final: 0.7391 (t0) REVERT: E 105 MET cc_start: 0.8026 (mmm) cc_final: 0.7807 (mmm) REVERT: E 126 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7052 (pm20) REVERT: E 227 GLU cc_start: 0.8184 (pt0) cc_final: 0.7921 (pt0) REVERT: E 262 MET cc_start: 0.5386 (ptm) cc_final: 0.5176 (ptt) REVERT: E 303 MET cc_start: 0.9281 (mmt) cc_final: 0.9074 (mmt) REVERT: E 322 PHE cc_start: 0.7771 (t80) cc_final: 0.7395 (t80) REVERT: E 401 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6460 (tpt-90) outliers start: 65 outliers final: 29 residues processed: 361 average time/residue: 0.9283 time to fit residues: 372.6221 Evaluate side-chains 339 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 302 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 401 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.3980 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 282 GLN B 62 ASN D 141 ASN D 180 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14510 Z= 0.211 Angle : 0.631 8.244 19680 Z= 0.314 Chirality : 0.046 0.169 2260 Planarity : 0.003 0.040 2435 Dihedral : 6.784 29.865 2195 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.58 % Allowed : 17.45 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.19), residues: 1710 helix: -1.80 (0.21), residues: 555 sheet: -0.38 (0.29), residues: 320 loop : -2.17 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.001 0.000 HIS A 125 PHE 0.022 0.001 PHE B 322 TYR 0.013 0.001 TYR A 317 ARG 0.003 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 318 time to evaluate : 1.594 Fit side-chains REVERT: A 43 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8571 (mtm180) REVERT: A 97 ASP cc_start: 0.8089 (m-30) cc_final: 0.7491 (t0) REVERT: A 126 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 130 ASP cc_start: 0.7913 (m-30) cc_final: 0.7443 (m-30) REVERT: A 138 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8177 (tttm) REVERT: A 206 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7744 (mttm) REVERT: A 210 ASP cc_start: 0.7977 (m-30) cc_final: 0.7521 (m-30) REVERT: A 303 MET cc_start: 0.9239 (mmt) cc_final: 0.8972 (mmt) REVERT: B 28 GLU cc_start: 0.8510 (tp30) cc_final: 0.8151 (tt0) REVERT: B 43 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.8619 (mtm180) REVERT: B 96 ASP cc_start: 0.8540 (m-30) cc_final: 0.8067 (m-30) REVERT: B 97 ASP cc_start: 0.8128 (m-30) cc_final: 0.7552 (t0) REVERT: B 113 ASP cc_start: 0.8540 (p0) cc_final: 0.8085 (p0) REVERT: B 126 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 229 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7753 (mtp85) REVERT: B 235 GLN cc_start: 0.8186 (mm110) cc_final: 0.7806 (mt0) REVERT: B 420 PHE cc_start: 0.8269 (t80) cc_final: 0.7904 (m-80) REVERT: C 28 GLU cc_start: 0.8483 (tp30) cc_final: 0.8214 (tt0) REVERT: C 31 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: C 72 MET cc_start: 0.8825 (mtt) cc_final: 0.8587 (mtt) REVERT: C 93 GLU cc_start: 0.8921 (pp20) cc_final: 0.8633 (pp20) REVERT: C 97 ASP cc_start: 0.8029 (m-30) cc_final: 0.7550 (t0) REVERT: C 113 ASP cc_start: 0.8462 (p0) cc_final: 0.8037 (p0) REVERT: C 126 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 130 ASP cc_start: 0.7760 (m-30) cc_final: 0.7475 (m-30) REVERT: C 181 ASP cc_start: 0.8199 (m-30) cc_final: 0.7861 (m-30) REVERT: C 206 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7766 (mttm) REVERT: C 210 ASP cc_start: 0.7917 (m-30) cc_final: 0.7621 (m-30) REVERT: C 227 GLU cc_start: 0.8281 (pt0) cc_final: 0.7832 (pt0) REVERT: C 243 MET cc_start: 0.7631 (tpp) cc_final: 0.7250 (mtt) REVERT: C 398 ARG cc_start: 0.6767 (mtt90) cc_final: 0.6247 (tpt170) REVERT: C 401 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6452 (tpt-90) REVERT: C 420 PHE cc_start: 0.8177 (t80) cc_final: 0.7935 (m-80) REVERT: D 28 GLU cc_start: 0.8711 (tp30) cc_final: 0.8403 (mt-10) REVERT: D 72 MET cc_start: 0.8806 (mtm) cc_final: 0.8578 (mtt) REVERT: D 75 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.6964 (mtp-110) REVERT: D 97 ASP cc_start: 0.8160 (m-30) cc_final: 0.7468 (t0) REVERT: D 126 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7272 (mt-10) REVERT: D 206 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7643 (mttm) REVERT: D 210 ASP cc_start: 0.7876 (m-30) cc_final: 0.7547 (m-30) REVERT: D 303 MET cc_start: 0.9298 (mmm) cc_final: 0.8990 (mmt) REVERT: D 322 PHE cc_start: 0.7744 (t80) cc_final: 0.7452 (t80) REVERT: D 391 MET cc_start: 0.6056 (tpt) cc_final: 0.5153 (ttp) REVERT: D 420 PHE cc_start: 0.7801 (t80) cc_final: 0.7495 (t80) REVERT: E 28 GLU cc_start: 0.8450 (tp30) cc_final: 0.8121 (tt0) REVERT: E 43 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.8654 (mtm180) REVERT: E 93 GLU cc_start: 0.8854 (pp20) cc_final: 0.8542 (pp20) REVERT: E 97 ASP cc_start: 0.8052 (m-30) cc_final: 0.7430 (t0) REVERT: E 105 MET cc_start: 0.8038 (mmm) cc_final: 0.7813 (mmm) REVERT: E 126 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7369 (mt-10) REVERT: E 210 ASP cc_start: 0.7930 (m-30) cc_final: 0.7631 (m-30) REVERT: E 227 GLU cc_start: 0.8134 (pt0) cc_final: 0.7804 (pt0) REVERT: E 243 MET cc_start: 0.7839 (tpp) cc_final: 0.7549 (mtt) REVERT: E 322 PHE cc_start: 0.7781 (t80) cc_final: 0.7412 (t80) REVERT: E 423 ILE cc_start: 0.8847 (mp) cc_final: 0.8583 (mp) outliers start: 70 outliers final: 33 residues processed: 360 average time/residue: 0.9841 time to fit residues: 398.1127 Evaluate side-chains 342 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 306 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.0470 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 140 optimal weight: 0.0170 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14510 Z= 0.175 Angle : 0.603 8.353 19680 Z= 0.299 Chirality : 0.044 0.162 2260 Planarity : 0.003 0.038 2435 Dihedral : 5.579 24.909 2195 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.38 % Allowed : 19.28 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.19), residues: 1710 helix: -1.36 (0.22), residues: 550 sheet: -0.30 (0.28), residues: 320 loop : -2.09 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.001 0.000 HIS A 125 PHE 0.023 0.001 PHE B 322 TYR 0.011 0.001 TYR A 317 ARG 0.003 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 325 time to evaluate : 1.417 Fit side-chains REVERT: A 43 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8586 (mtm180) REVERT: A 96 ASP cc_start: 0.8511 (m-30) cc_final: 0.8056 (m-30) REVERT: A 97 ASP cc_start: 0.8067 (m-30) cc_final: 0.7478 (t0) REVERT: A 126 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 130 ASP cc_start: 0.7800 (m-30) cc_final: 0.7319 (m-30) REVERT: A 138 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8153 (tttm) REVERT: A 206 LYS cc_start: 0.8227 (mtpt) cc_final: 0.8006 (mttt) REVERT: A 210 ASP cc_start: 0.7960 (m-30) cc_final: 0.7487 (m-30) REVERT: A 227 GLU cc_start: 0.8225 (pt0) cc_final: 0.7887 (pt0) REVERT: A 229 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7958 (mtp85) REVERT: A 401 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6243 (tpt-90) REVERT: A 419 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7297 (mp) REVERT: A 420 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: B 28 GLU cc_start: 0.8495 (tp30) cc_final: 0.8137 (tt0) REVERT: B 43 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.8758 (mtm180) REVERT: B 96 ASP cc_start: 0.8551 (m-30) cc_final: 0.8070 (m-30) REVERT: B 97 ASP cc_start: 0.8099 (m-30) cc_final: 0.7536 (t0) REVERT: B 113 ASP cc_start: 0.8490 (p0) cc_final: 0.8053 (p0) REVERT: B 126 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7321 (mt-10) REVERT: B 160 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6804 (p0) REVERT: B 229 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7786 (mtp85) REVERT: B 235 GLN cc_start: 0.8229 (mm110) cc_final: 0.7841 (mt0) REVERT: B 243 MET cc_start: 0.7861 (tpp) cc_final: 0.7566 (mtt) REVERT: B 316 GLU cc_start: 0.6283 (tm-30) cc_final: 0.6069 (tm-30) REVERT: B 420 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: C 28 GLU cc_start: 0.8474 (tp30) cc_final: 0.8190 (tt0) REVERT: C 31 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: C 72 MET cc_start: 0.8797 (mtt) cc_final: 0.8535 (mtt) REVERT: C 97 ASP cc_start: 0.8015 (m-30) cc_final: 0.7561 (t0) REVERT: C 113 ASP cc_start: 0.8389 (p0) cc_final: 0.7980 (p0) REVERT: C 126 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7086 (mt-10) REVERT: C 130 ASP cc_start: 0.7726 (m-30) cc_final: 0.7512 (m-30) REVERT: C 181 ASP cc_start: 0.8170 (m-30) cc_final: 0.7862 (m-30) REVERT: C 206 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7790 (mttm) REVERT: C 210 ASP cc_start: 0.7937 (m-30) cc_final: 0.7588 (m-30) REVERT: C 227 GLU cc_start: 0.8181 (pt0) cc_final: 0.7801 (pt0) REVERT: C 243 MET cc_start: 0.7803 (tpp) cc_final: 0.7427 (mtt) REVERT: C 398 ARG cc_start: 0.6694 (mtt90) cc_final: 0.6200 (tpt170) REVERT: D 28 GLU cc_start: 0.8704 (tp30) cc_final: 0.8344 (tt0) REVERT: D 72 MET cc_start: 0.8805 (mtm) cc_final: 0.8598 (mtt) REVERT: D 75 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.6966 (mtp-110) REVERT: D 97 ASP cc_start: 0.8120 (m-30) cc_final: 0.7464 (t0) REVERT: D 126 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7214 (mt-10) REVERT: D 206 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7639 (mttm) REVERT: D 210 ASP cc_start: 0.7823 (m-30) cc_final: 0.7525 (m-30) REVERT: D 227 GLU cc_start: 0.8284 (pt0) cc_final: 0.8016 (pt0) REVERT: D 243 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7518 (mtt) REVERT: D 303 MET cc_start: 0.9260 (mmm) cc_final: 0.8950 (mmt) REVERT: D 391 MET cc_start: 0.6142 (tpt) cc_final: 0.5169 (ptm) REVERT: E 28 GLU cc_start: 0.8422 (tp30) cc_final: 0.8071 (tt0) REVERT: E 43 ARG cc_start: 0.8955 (mtm-85) cc_final: 0.8652 (mtm180) REVERT: E 93 GLU cc_start: 0.8862 (pp20) cc_final: 0.8566 (pp20) REVERT: E 97 ASP cc_start: 0.8038 (m-30) cc_final: 0.7418 (t0) REVERT: E 105 MET cc_start: 0.8034 (mmm) cc_final: 0.7782 (mmm) REVERT: E 108 SER cc_start: 0.8452 (t) cc_final: 0.8205 (p) REVERT: E 126 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7306 (mt-10) REVERT: E 210 ASP cc_start: 0.7980 (m-30) cc_final: 0.7649 (m-30) REVERT: E 227 GLU cc_start: 0.8098 (pt0) cc_final: 0.7822 (pt0) REVERT: E 243 MET cc_start: 0.7878 (tpp) cc_final: 0.7599 (mtt) REVERT: E 423 ILE cc_start: 0.8797 (mp) cc_final: 0.8522 (mp) outliers start: 67 outliers final: 27 residues processed: 361 average time/residue: 1.0000 time to fit residues: 402.9154 Evaluate side-chains 324 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 288 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 164 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 76 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.5312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN E 58 ASN E 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14510 Z= 0.181 Angle : 0.615 9.269 19680 Z= 0.304 Chirality : 0.044 0.169 2260 Planarity : 0.003 0.034 2435 Dihedral : 5.105 19.904 2195 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.31 % Allowed : 20.46 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1710 helix: -1.20 (0.23), residues: 555 sheet: -0.18 (0.28), residues: 320 loop : -1.97 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.001 0.000 HIS E 125 PHE 0.021 0.001 PHE B 322 TYR 0.011 0.001 TYR A 317 ARG 0.002 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 295 time to evaluate : 1.612 Fit side-chains REVERT: A 43 ARG cc_start: 0.8906 (mtm-85) cc_final: 0.8599 (mtm180) REVERT: A 96 ASP cc_start: 0.8508 (m-30) cc_final: 0.8048 (m-30) REVERT: A 97 ASP cc_start: 0.8113 (m-30) cc_final: 0.7572 (t0) REVERT: A 126 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7104 (mt-10) REVERT: A 130 ASP cc_start: 0.7795 (m-30) cc_final: 0.7312 (m-30) REVERT: A 138 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8138 (tttm) REVERT: A 156 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7053 (mmt) REVERT: A 179 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8439 (tpt) REVERT: A 206 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7738 (mttm) REVERT: A 210 ASP cc_start: 0.7905 (m-30) cc_final: 0.7451 (m-30) REVERT: A 229 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8024 (mtp85) REVERT: A 391 MET cc_start: 0.6159 (tpt) cc_final: 0.5904 (tpt) REVERT: A 401 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6282 (tpt-90) REVERT: A 419 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7303 (mp) REVERT: A 420 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: B 28 GLU cc_start: 0.8479 (tp30) cc_final: 0.8125 (tt0) REVERT: B 96 ASP cc_start: 0.8542 (m-30) cc_final: 0.8047 (m-30) REVERT: B 97 ASP cc_start: 0.8093 (m-30) cc_final: 0.7557 (t0) REVERT: B 113 ASP cc_start: 0.8496 (p0) cc_final: 0.8053 (p0) REVERT: B 126 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 156 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7262 (mmt) REVERT: B 229 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7782 (mtp85) REVERT: B 235 GLN cc_start: 0.8227 (mm110) cc_final: 0.7829 (mt0) REVERT: B 420 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: C 28 GLU cc_start: 0.8468 (tp30) cc_final: 0.8139 (tt0) REVERT: C 31 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: C 72 MET cc_start: 0.8823 (mtt) cc_final: 0.8558 (mtt) REVERT: C 97 ASP cc_start: 0.7978 (m-30) cc_final: 0.7540 (t0) REVERT: C 113 ASP cc_start: 0.8417 (p0) cc_final: 0.7991 (p0) REVERT: C 126 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7108 (mt-10) REVERT: C 130 ASP cc_start: 0.7719 (m-30) cc_final: 0.7440 (m-30) REVERT: C 181 ASP cc_start: 0.8223 (m-30) cc_final: 0.7905 (m-30) REVERT: C 206 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7724 (mttm) REVERT: C 210 ASP cc_start: 0.7914 (m-30) cc_final: 0.7562 (m-30) REVERT: C 227 GLU cc_start: 0.8149 (pt0) cc_final: 0.7803 (pt0) REVERT: C 243 MET cc_start: 0.7760 (tpp) cc_final: 0.7055 (mtt) REVERT: C 398 ARG cc_start: 0.6619 (mtt90) cc_final: 0.6129 (tpt170) REVERT: C 419 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7232 (mp) REVERT: D 28 GLU cc_start: 0.8691 (tp30) cc_final: 0.8326 (tt0) REVERT: D 72 MET cc_start: 0.8811 (mtm) cc_final: 0.8590 (mtt) REVERT: D 75 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.6976 (mtp-110) REVERT: D 97 ASP cc_start: 0.8109 (m-30) cc_final: 0.7505 (t0) REVERT: D 126 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7245 (mt-10) REVERT: D 206 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7686 (mttm) REVERT: D 210 ASP cc_start: 0.7779 (m-30) cc_final: 0.7471 (m-30) REVERT: D 227 GLU cc_start: 0.8270 (pt0) cc_final: 0.8061 (pt0) REVERT: D 303 MET cc_start: 0.9255 (mmm) cc_final: 0.8943 (mmt) REVERT: D 391 MET cc_start: 0.6177 (tpt) cc_final: 0.5297 (ttp) REVERT: E 28 GLU cc_start: 0.8417 (tp30) cc_final: 0.8071 (tt0) REVERT: E 43 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8591 (mtm180) REVERT: E 93 GLU cc_start: 0.8882 (pp20) cc_final: 0.8610 (pp20) REVERT: E 97 ASP cc_start: 0.7996 (m-30) cc_final: 0.7396 (t0) REVERT: E 105 MET cc_start: 0.8041 (mmm) cc_final: 0.7789 (mmm) REVERT: E 108 SER cc_start: 0.8464 (t) cc_final: 0.8215 (p) REVERT: E 126 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 243 MET cc_start: 0.7884 (tpp) cc_final: 0.7585 (mtt) REVERT: E 423 ILE cc_start: 0.8801 (mp) cc_final: 0.8538 (mp) outliers start: 66 outliers final: 31 residues processed: 331 average time/residue: 1.0376 time to fit residues: 382.7238 Evaluate side-chains 340 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 298 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 0.0470 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN B 261 ASN D 261 ASN E 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14510 Z= 0.224 Angle : 0.636 10.925 19680 Z= 0.316 Chirality : 0.045 0.176 2260 Planarity : 0.003 0.037 2435 Dihedral : 5.127 40.814 2195 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.71 % Allowed : 20.78 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1710 helix: -1.15 (0.23), residues: 555 sheet: -0.27 (0.27), residues: 365 loop : -1.84 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.001 0.000 HIS A 231 PHE 0.019 0.001 PHE B 322 TYR 0.011 0.001 TYR D 317 ARG 0.006 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 316 time to evaluate : 1.478 Fit side-chains REVERT: A 43 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.8592 (mtm180) REVERT: A 96 ASP cc_start: 0.8516 (m-30) cc_final: 0.7882 (m-30) REVERT: A 97 ASP cc_start: 0.8119 (m-30) cc_final: 0.7602 (t0) REVERT: A 126 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7196 (mt-10) REVERT: A 179 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8476 (tpt) REVERT: A 181 ASP cc_start: 0.8247 (m-30) cc_final: 0.8006 (m-30) REVERT: A 206 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7808 (mmtp) REVERT: A 210 ASP cc_start: 0.7879 (m-30) cc_final: 0.7397 (m-30) REVERT: A 229 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8116 (mtp85) REVERT: A 391 MET cc_start: 0.6093 (tpt) cc_final: 0.5853 (tpt) REVERT: B 28 GLU cc_start: 0.8474 (tp30) cc_final: 0.8128 (tt0) REVERT: B 96 ASP cc_start: 0.8557 (m-30) cc_final: 0.8320 (m-30) REVERT: B 97 ASP cc_start: 0.8092 (m-30) cc_final: 0.7577 (t0) REVERT: B 113 ASP cc_start: 0.8498 (p0) cc_final: 0.8059 (p0) REVERT: B 126 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7339 (mt-10) REVERT: B 206 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7881 (mttm) REVERT: B 229 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7758 (mtp85) REVERT: B 235 GLN cc_start: 0.8243 (mm110) cc_final: 0.7841 (mt0) REVERT: B 258 PHE cc_start: 0.7472 (m-10) cc_final: 0.7260 (m-10) REVERT: B 316 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6025 (tm-30) REVERT: B 401 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6577 (tpt-90) REVERT: B 420 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: C 28 GLU cc_start: 0.8471 (tp30) cc_final: 0.8163 (tt0) REVERT: C 31 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: C 72 MET cc_start: 0.8833 (mtt) cc_final: 0.8583 (mtt) REVERT: C 93 GLU cc_start: 0.8879 (pp20) cc_final: 0.8612 (pp20) REVERT: C 97 ASP cc_start: 0.7981 (m-30) cc_final: 0.7586 (t0) REVERT: C 113 ASP cc_start: 0.8404 (p0) cc_final: 0.8000 (p0) REVERT: C 126 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7119 (mt-10) REVERT: C 130 ASP cc_start: 0.7761 (m-30) cc_final: 0.7484 (m-30) REVERT: C 181 ASP cc_start: 0.8263 (m-30) cc_final: 0.7917 (m-30) REVERT: C 206 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7731 (mttm) REVERT: C 210 ASP cc_start: 0.7903 (m-30) cc_final: 0.7538 (m-30) REVERT: C 227 GLU cc_start: 0.8153 (pt0) cc_final: 0.7798 (pt0) REVERT: C 243 MET cc_start: 0.7796 (tpp) cc_final: 0.7052 (mtt) REVERT: C 398 ARG cc_start: 0.6599 (mtt90) cc_final: 0.6141 (tpt170) REVERT: D 28 GLU cc_start: 0.8691 (tp30) cc_final: 0.8402 (mt-10) REVERT: D 72 MET cc_start: 0.8842 (mtm) cc_final: 0.8591 (mtt) REVERT: D 75 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.6976 (mtp-110) REVERT: D 97 ASP cc_start: 0.8089 (m-30) cc_final: 0.7507 (t0) REVERT: D 126 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7180 (mt-10) REVERT: D 206 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7705 (mttm) REVERT: D 210 ASP cc_start: 0.7823 (m-30) cc_final: 0.7521 (m-30) REVERT: D 303 MET cc_start: 0.9249 (mmm) cc_final: 0.8910 (mmt) REVERT: D 391 MET cc_start: 0.6193 (tpt) cc_final: 0.5312 (ttp) REVERT: D 420 PHE cc_start: 0.7666 (t80) cc_final: 0.7378 (t80) REVERT: E 28 GLU cc_start: 0.8407 (tp30) cc_final: 0.8056 (tt0) REVERT: E 43 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8647 (mtm180) REVERT: E 93 GLU cc_start: 0.8885 (pp20) cc_final: 0.8586 (pp20) REVERT: E 97 ASP cc_start: 0.7953 (m-30) cc_final: 0.7380 (t0) REVERT: E 105 MET cc_start: 0.8064 (mmm) cc_final: 0.7798 (mmm) REVERT: E 108 SER cc_start: 0.8491 (t) cc_final: 0.8224 (p) REVERT: E 126 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 243 MET cc_start: 0.7922 (tpp) cc_final: 0.7579 (mtt) REVERT: E 322 PHE cc_start: 0.7838 (t80) cc_final: 0.7469 (t80) REVERT: E 423 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8519 (mp) outliers start: 72 outliers final: 44 residues processed: 357 average time/residue: 1.0194 time to fit residues: 405.1597 Evaluate side-chains 349 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 298 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14510 Z= 0.216 Angle : 0.638 14.483 19680 Z= 0.317 Chirality : 0.045 0.226 2260 Planarity : 0.003 0.035 2435 Dihedral : 5.126 46.880 2195 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.91 % Rotamer: Outliers : 4.12 % Allowed : 21.83 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.86 (0.20), residues: 1710 helix: -1.09 (0.23), residues: 555 sheet: -0.21 (0.27), residues: 365 loop : -1.79 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.001 0.000 HIS D 125 PHE 0.018 0.001 PHE B 322 TYR 0.013 0.001 TYR D 213 ARG 0.005 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 296 time to evaluate : 1.681 Fit side-chains REVERT: A 43 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8574 (mtm180) REVERT: A 96 ASP cc_start: 0.8314 (m-30) cc_final: 0.7890 (m-30) REVERT: A 97 ASP cc_start: 0.8144 (m-30) cc_final: 0.7617 (t0) REVERT: A 126 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7076 (mt-10) REVERT: A 130 ASP cc_start: 0.7872 (m-30) cc_final: 0.7279 (m-30) REVERT: A 206 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7763 (mttm) REVERT: A 210 ASP cc_start: 0.7861 (m-30) cc_final: 0.7367 (m-30) REVERT: A 229 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8119 (mtp85) REVERT: A 391 MET cc_start: 0.6121 (tpt) cc_final: 0.5889 (tpt) REVERT: A 420 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: B 28 GLU cc_start: 0.8467 (tp30) cc_final: 0.8114 (tt0) REVERT: B 96 ASP cc_start: 0.8543 (m-30) cc_final: 0.8291 (m-30) REVERT: B 97 ASP cc_start: 0.8068 (m-30) cc_final: 0.7582 (t0) REVERT: B 113 ASP cc_start: 0.8490 (p0) cc_final: 0.8054 (p0) REVERT: B 126 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7340 (mt-10) REVERT: B 206 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7914 (mttm) REVERT: B 229 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7757 (mtp85) REVERT: B 235 GLN cc_start: 0.8280 (mm110) cc_final: 0.7935 (mt0) REVERT: B 279 MET cc_start: 0.6942 (tpp) cc_final: 0.6457 (mpp) REVERT: B 401 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6544 (tpt-90) REVERT: B 420 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: C 28 GLU cc_start: 0.8462 (tp30) cc_final: 0.8157 (tt0) REVERT: C 31 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: C 72 MET cc_start: 0.8845 (mtt) cc_final: 0.8593 (mtt) REVERT: C 97 ASP cc_start: 0.7949 (m-30) cc_final: 0.7597 (t0) REVERT: C 113 ASP cc_start: 0.8391 (p0) cc_final: 0.7993 (p0) REVERT: C 126 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7113 (mt-10) REVERT: C 130 ASP cc_start: 0.7767 (m-30) cc_final: 0.7496 (m-30) REVERT: C 181 ASP cc_start: 0.8258 (m-30) cc_final: 0.7912 (m-30) REVERT: C 206 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7710 (mttm) REVERT: C 210 ASP cc_start: 0.7887 (m-30) cc_final: 0.7510 (m-30) REVERT: C 243 MET cc_start: 0.7803 (tpp) cc_final: 0.7074 (mtt) REVERT: C 398 ARG cc_start: 0.6593 (mtt90) cc_final: 0.6140 (tpt170) REVERT: D 28 GLU cc_start: 0.8688 (tp30) cc_final: 0.8364 (tt0) REVERT: D 72 MET cc_start: 0.8815 (mtm) cc_final: 0.8577 (mtt) REVERT: D 75 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.6985 (mtp-110) REVERT: D 97 ASP cc_start: 0.8071 (m-30) cc_final: 0.7515 (t0) REVERT: D 126 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7172 (mt-10) REVERT: D 206 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7702 (mttm) REVERT: D 208 GLU cc_start: 0.8122 (tp30) cc_final: 0.7638 (tm-30) REVERT: D 210 ASP cc_start: 0.7715 (m-30) cc_final: 0.7479 (m-30) REVERT: D 303 MET cc_start: 0.9247 (mmm) cc_final: 0.8937 (mmt) REVERT: D 420 PHE cc_start: 0.7650 (t80) cc_final: 0.7377 (t80) REVERT: E 28 GLU cc_start: 0.8418 (tp30) cc_final: 0.8076 (tt0) REVERT: E 43 ARG cc_start: 0.8972 (mtm-85) cc_final: 0.8671 (mtm180) REVERT: E 93 GLU cc_start: 0.8873 (pp20) cc_final: 0.8607 (pp20) REVERT: E 97 ASP cc_start: 0.7955 (m-30) cc_final: 0.7422 (t0) REVERT: E 105 MET cc_start: 0.8070 (mmm) cc_final: 0.7799 (mmm) REVERT: E 108 SER cc_start: 0.8491 (t) cc_final: 0.8218 (p) REVERT: E 126 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7327 (mt-10) REVERT: E 243 MET cc_start: 0.7906 (tpp) cc_final: 0.7505 (mtt) REVERT: E 262 MET cc_start: 0.6072 (ptp) cc_final: 0.5475 (pmm) REVERT: E 322 PHE cc_start: 0.7801 (t80) cc_final: 0.7411 (t80) REVERT: E 423 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8506 (mp) outliers start: 63 outliers final: 43 residues processed: 332 average time/residue: 1.0372 time to fit residues: 383.4664 Evaluate side-chains 340 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 290 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN B 82 GLN C 82 GLN C 261 ASN D 82 GLN E 62 ASN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 14510 Z= 0.336 Angle : 0.694 10.333 19680 Z= 0.347 Chirality : 0.047 0.207 2260 Planarity : 0.004 0.039 2435 Dihedral : 5.393 48.648 2195 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 4.44 % Allowed : 21.31 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.86 (0.20), residues: 1710 helix: -1.17 (0.22), residues: 555 sheet: -0.20 (0.28), residues: 370 loop : -1.74 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 186 HIS 0.002 0.001 HIS D 217 PHE 0.017 0.002 PHE B 322 TYR 0.020 0.002 TYR C 213 ARG 0.005 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 292 time to evaluate : 1.541 Fit side-chains REVERT: A 96 ASP cc_start: 0.8379 (m-30) cc_final: 0.7937 (m-30) REVERT: A 97 ASP cc_start: 0.8159 (m-30) cc_final: 0.7637 (t0) REVERT: A 113 ASP cc_start: 0.8628 (p0) cc_final: 0.8285 (p0) REVERT: A 126 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 130 ASP cc_start: 0.7950 (m-30) cc_final: 0.7376 (m-30) REVERT: A 173 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 206 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7845 (mmtp) REVERT: A 210 ASP cc_start: 0.7855 (m-30) cc_final: 0.7345 (m-30) REVERT: A 229 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8053 (mtp85) REVERT: A 391 MET cc_start: 0.6271 (tpt) cc_final: 0.6057 (tpt) REVERT: A 420 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: B 28 GLU cc_start: 0.8485 (tp30) cc_final: 0.8108 (tt0) REVERT: B 96 ASP cc_start: 0.8580 (m-30) cc_final: 0.8310 (m-30) REVERT: B 97 ASP cc_start: 0.8094 (m-30) cc_final: 0.7617 (t0) REVERT: B 113 ASP cc_start: 0.8541 (p0) cc_final: 0.8140 (p0) REVERT: B 126 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 229 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7839 (mmt90) REVERT: B 235 GLN cc_start: 0.8270 (mm110) cc_final: 0.7799 (mt0) REVERT: B 316 GLU cc_start: 0.6292 (tm-30) cc_final: 0.6060 (tm-30) REVERT: B 401 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6565 (tpt-90) REVERT: B 420 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: C 28 GLU cc_start: 0.8482 (tp30) cc_final: 0.8168 (tt0) REVERT: C 31 ASP cc_start: 0.8699 (m-30) cc_final: 0.8333 (m-30) REVERT: C 72 MET cc_start: 0.8888 (mtt) cc_final: 0.8621 (mtt) REVERT: C 97 ASP cc_start: 0.7992 (m-30) cc_final: 0.7691 (t0) REVERT: C 113 ASP cc_start: 0.8472 (p0) cc_final: 0.8077 (p0) REVERT: C 126 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7207 (mt-10) REVERT: C 130 ASP cc_start: 0.7911 (m-30) cc_final: 0.7659 (m-30) REVERT: C 181 ASP cc_start: 0.8288 (m-30) cc_final: 0.7968 (m-30) REVERT: C 206 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7664 (mttm) REVERT: C 210 ASP cc_start: 0.7871 (m-30) cc_final: 0.7471 (m-30) REVERT: C 398 ARG cc_start: 0.6623 (mtt90) cc_final: 0.6177 (tpt170) REVERT: D 28 GLU cc_start: 0.8716 (tp30) cc_final: 0.8373 (mt-10) REVERT: D 72 MET cc_start: 0.8826 (mtm) cc_final: 0.8539 (mtt) REVERT: D 75 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7109 (mtp-110) REVERT: D 97 ASP cc_start: 0.8077 (m-30) cc_final: 0.7537 (t0) REVERT: D 126 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7148 (mt-10) REVERT: D 206 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7710 (mttm) REVERT: D 210 ASP cc_start: 0.7785 (m-30) cc_final: 0.7463 (m-30) REVERT: D 303 MET cc_start: 0.9242 (mmm) cc_final: 0.8903 (mmt) REVERT: D 391 MET cc_start: 0.6001 (tpt) cc_final: 0.5245 (ttp) REVERT: D 401 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6515 (mmm160) REVERT: D 420 PHE cc_start: 0.7700 (t80) cc_final: 0.7407 (t80) REVERT: E 28 GLU cc_start: 0.8419 (tp30) cc_final: 0.8098 (tt0) REVERT: E 43 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8620 (mtm180) REVERT: E 93 GLU cc_start: 0.8868 (pp20) cc_final: 0.8618 (pp20) REVERT: E 97 ASP cc_start: 0.7983 (m-30) cc_final: 0.7492 (t0) REVERT: E 105 MET cc_start: 0.8084 (mmm) cc_final: 0.7881 (mmm) REVERT: E 126 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7347 (mt-10) REVERT: E 243 MET cc_start: 0.8039 (tpp) cc_final: 0.7680 (mtt) REVERT: E 420 PHE cc_start: 0.7493 (t80) cc_final: 0.7248 (t80) REVERT: E 423 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 68 outliers final: 44 residues processed: 335 average time/residue: 1.0454 time to fit residues: 388.2755 Evaluate side-chains 329 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 278 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 418 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN B 82 GLN C 62 ASN C 82 GLN D 62 ASN D 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14510 Z= 0.197 Angle : 0.645 9.639 19680 Z= 0.321 Chirality : 0.045 0.187 2260 Planarity : 0.003 0.034 2435 Dihedral : 5.134 47.732 2195 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 3.01 % Allowed : 23.27 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.71 (0.20), residues: 1710 helix: -0.98 (0.23), residues: 555 sheet: -0.12 (0.27), residues: 365 loop : -1.69 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 186 HIS 0.001 0.000 HIS D 125 PHE 0.032 0.001 PHE B 322 TYR 0.010 0.001 TYR A 317 ARG 0.005 0.000 ARG A 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 288 time to evaluate : 2.021 Fit side-chains REVERT: A 43 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8573 (mtm180) REVERT: A 96 ASP cc_start: 0.8311 (m-30) cc_final: 0.7859 (m-30) REVERT: A 97 ASP cc_start: 0.8138 (m-30) cc_final: 0.7726 (t0) REVERT: A 126 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 130 ASP cc_start: 0.7934 (m-30) cc_final: 0.7419 (m-30) REVERT: A 173 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 206 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7796 (mttm) REVERT: A 210 ASP cc_start: 0.7850 (m-30) cc_final: 0.7285 (m-30) REVERT: A 229 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7950 (mtp85) REVERT: A 391 MET cc_start: 0.6308 (tpt) cc_final: 0.6098 (tpt) REVERT: A 418 ASN cc_start: 0.7523 (m-40) cc_final: 0.7283 (m-40) REVERT: A 420 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: B 28 GLU cc_start: 0.8458 (tp30) cc_final: 0.8104 (tt0) REVERT: B 96 ASP cc_start: 0.8525 (m-30) cc_final: 0.8239 (m-30) REVERT: B 97 ASP cc_start: 0.8078 (m-30) cc_final: 0.7659 (t0) REVERT: B 113 ASP cc_start: 0.8520 (p0) cc_final: 0.8090 (p0) REVERT: B 126 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 206 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7809 (mttm) REVERT: B 229 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7765 (mtp85) REVERT: B 235 GLN cc_start: 0.8277 (mm110) cc_final: 0.7838 (mt0) REVERT: B 401 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6563 (tpt-90) REVERT: B 420 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: C 28 GLU cc_start: 0.8468 (tp30) cc_final: 0.8161 (tt0) REVERT: C 31 ASP cc_start: 0.8660 (m-30) cc_final: 0.8278 (m-30) REVERT: C 72 MET cc_start: 0.8868 (mtt) cc_final: 0.8624 (mtt) REVERT: C 97 ASP cc_start: 0.7951 (m-30) cc_final: 0.7695 (t0) REVERT: C 113 ASP cc_start: 0.8394 (p0) cc_final: 0.8001 (p0) REVERT: C 126 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6942 (mt-10) REVERT: C 130 ASP cc_start: 0.7765 (m-30) cc_final: 0.7331 (m-30) REVERT: C 181 ASP cc_start: 0.8225 (m-30) cc_final: 0.7894 (m-30) REVERT: C 206 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7720 (mttm) REVERT: C 210 ASP cc_start: 0.7830 (m-30) cc_final: 0.7413 (m-30) REVERT: C 243 MET cc_start: 0.7811 (tpp) cc_final: 0.7492 (mtt) REVERT: C 398 ARG cc_start: 0.6557 (mtt90) cc_final: 0.6139 (tpt170) REVERT: D 28 GLU cc_start: 0.8691 (tp30) cc_final: 0.8343 (mt-10) REVERT: D 72 MET cc_start: 0.8801 (mtm) cc_final: 0.8569 (mtt) REVERT: D 75 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.7089 (mtp-110) REVERT: D 97 ASP cc_start: 0.8045 (m-30) cc_final: 0.7564 (t0) REVERT: D 126 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7141 (mt-10) REVERT: D 130 ASP cc_start: 0.7889 (m-30) cc_final: 0.7426 (m-30) REVERT: D 206 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7715 (mttm) REVERT: D 210 ASP cc_start: 0.7732 (m-30) cc_final: 0.7413 (m-30) REVERT: D 303 MET cc_start: 0.9228 (mmm) cc_final: 0.8898 (mmt) REVERT: D 316 GLU cc_start: 0.6569 (tm-30) cc_final: 0.6343 (tm-30) REVERT: D 391 MET cc_start: 0.6058 (tpt) cc_final: 0.5342 (ttp) REVERT: D 420 PHE cc_start: 0.7653 (t80) cc_final: 0.7360 (t80) REVERT: E 28 GLU cc_start: 0.8405 (tp30) cc_final: 0.8071 (tt0) REVERT: E 43 ARG cc_start: 0.8967 (mtm-85) cc_final: 0.8685 (mtm180) REVERT: E 93 GLU cc_start: 0.8844 (pp20) cc_final: 0.8618 (pp20) REVERT: E 97 ASP cc_start: 0.7906 (m-30) cc_final: 0.7482 (t0) REVERT: E 108 SER cc_start: 0.8484 (t) cc_final: 0.8189 (p) REVERT: E 126 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7310 (mt-10) REVERT: E 243 MET cc_start: 0.7940 (tpp) cc_final: 0.7503 (mtt) REVERT: E 398 ARG cc_start: 0.6520 (mtt90) cc_final: 0.6058 (tpt170) REVERT: E 423 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8487 (mp) outliers start: 46 outliers final: 37 residues processed: 316 average time/residue: 1.1108 time to fit residues: 388.3977 Evaluate side-chains 334 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 291 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 418 ASN Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN D 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110803 restraints weight = 16490.711| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.35 r_work: 0.3057 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14510 Z= 0.210 Angle : 0.646 11.721 19680 Z= 0.320 Chirality : 0.045 0.210 2260 Planarity : 0.003 0.033 2435 Dihedral : 5.042 47.542 2195 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.33 % Favored : 95.44 % Rotamer: Outliers : 3.27 % Allowed : 23.27 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1710 helix: -0.90 (0.23), residues: 555 sheet: -0.04 (0.27), residues: 365 loop : -1.68 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 186 HIS 0.001 0.000 HIS D 125 PHE 0.031 0.001 PHE B 322 TYR 0.010 0.001 TYR D 317 ARG 0.005 0.000 ARG A 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6367.06 seconds wall clock time: 112 minutes 25.22 seconds (6745.22 seconds total)