Starting phenix.real_space_refine on Sat Mar 16 08:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm1_20383/03_2024/6pm1_20383_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm1_20383/03_2024/6pm1_20383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm1_20383/03_2024/6pm1_20383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm1_20383/03_2024/6pm1_20383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm1_20383/03_2024/6pm1_20383_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm1_20383/03_2024/6pm1_20383_updated.pdb" } resolution = 3.0 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= 0.045 sd= 4.739 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 105 5.16 5 C 9215 2.51 5 N 2285 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14160 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.74, per 1000 atoms: 0.55 Number of scatterers: 14160 At special positions: 0 Unit cell: (106.167, 107.813, 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 105 16.00 O 2555 8.00 N 2285 7.00 C 9215 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=2.05 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.05 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.05 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.05 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 2.4 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 20 sheets defined 33.5% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.591A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.730A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.690A 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 236 through 242 removed outlier: 3.758A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.528A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.914A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 321 removed outlier: 4.035A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 405 removed outlier: 4.352A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 removed outlier: 4.285A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 removed outlier: 3.591A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.731A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.759A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.528A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.914A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 321 removed outlier: 4.035A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 removed outlier: 4.351A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 422 removed outlier: 4.284A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 33 removed outlier: 3.590A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.731A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 236 through 242 removed outlier: 3.759A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.529A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.914A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 321 removed outlier: 4.035A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 405 removed outlier: 4.351A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 422 removed outlier: 4.284A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.591A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.729A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 236 through 242 removed outlier: 3.758A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.529A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.915A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 321 removed outlier: 4.035A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 405 removed outlier: 4.350A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 400 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 422 removed outlier: 4.283A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 33 removed outlier: 3.590A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.730A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.759A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 255 removed outlier: 3.528A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.915A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 321 removed outlier: 4.036A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 4.351A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 404 " --> pdb=" O LYS E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 422 removed outlier: 4.283A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.151A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (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 114 through 116 Processing sheet with id= D, first strand: chain 'A' and resid 211 through 213 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.152A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= G, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= H, first strand: chain 'B' and resid 211 through 213 Processing sheet with id= I, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.152A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= K, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= L, first strand: chain 'C' and resid 211 through 213 Processing sheet with id= M, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.152A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= O, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= P, first strand: chain 'D' and resid 211 through 213 Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.151A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= S, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'E' and resid 211 through 213 475 hydrogen bonds defined for protein. 1410 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: 4.32 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4190 1.34 - 1.46: 3705 1.46 - 1.59: 6435 1.59 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 14505 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 14500 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.67: 385 105.67 - 112.88: 7568 112.88 - 120.09: 5647 120.09 - 127.30: 5911 127.30 - 134.51: 174 Bond angle restraints: 19685 Sorted by residual: angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 126.45 134.51 -8.06 1.77e+00 3.19e-01 2.07e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 126.45 134.51 -8.06 1.77e+00 3.19e-01 2.07e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 126.45 134.50 -8.05 1.77e+00 3.19e-01 2.07e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 126.45 134.49 -8.04 1.77e+00 3.19e-01 2.06e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 126.45 134.45 -8.00 1.77e+00 3.19e-01 2.04e+01 ... (remaining 19680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 8605 22.01 - 44.02: 205 44.02 - 66.02: 0 66.02 - 88.03: 35 88.03 - 110.04: 20 Dihedral angle restraints: 8865 sinusoidal: 3750 harmonic: 5115 Sorted by residual: 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 -150.06 -29.94 0 5.00e+00 4.00e-02 3.58e+01 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 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ASN B 160 " pdb=" C ASN B 160 " pdb=" N PHE B 161 " pdb=" CA PHE B 161 " ideal model delta harmonic sigma weight residual -180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 8862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1588 0.057 - 0.115: 532 0.115 - 0.172: 105 0.172 - 0.229: 23 0.229 - 0.287: 12 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+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 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 410 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO E 411 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 411 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 411 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 411 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO C 411 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " -0.037 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4597 2.84 - 3.36: 11913 3.36 - 3.87: 22771 3.87 - 4.39: 27367 4.39 - 4.90: 45917 Nonbonded interactions: 112565 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.326 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.326 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.326 2.440 ... (remaining 112560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 7.760 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 40.100 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 14505 Z= 0.506 Angle : 1.041 11.856 19685 Z= 0.521 Chirality : 0.061 0.287 2260 Planarity : 0.008 0.067 2430 Dihedral : 13.059 110.039 5515 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -4.95 (0.15), residues: 1710 helix: -4.96 (0.06), residues: 585 sheet: -2.09 (0.23), residues: 380 loop : -2.25 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 110 HIS 0.005 0.001 HIS C 231 PHE 0.023 0.003 PHE E 115 TYR 0.022 0.003 TYR B 144 ARG 0.009 0.001 ARG D 135 *********************** 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 463 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8371 (ptt) cc_final: 0.7694 (ptt) REVERT: A 126 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 210 ASP cc_start: 0.7724 (m-30) cc_final: 0.7470 (m-30) REVERT: A 233 GLU cc_start: 0.6866 (tt0) cc_final: 0.6486 (mt-10) REVERT: A 303 MET cc_start: 0.8805 (mmt) cc_final: 0.8342 (mmt) REVERT: A 415 LEU cc_start: 0.7607 (tt) cc_final: 0.7382 (tm) REVERT: A 420 PHE cc_start: 0.7178 (m-10) cc_final: 0.6909 (t80) REVERT: B 24 MET cc_start: 0.8379 (ptt) cc_final: 0.7623 (ptt) REVERT: B 41 ASP cc_start: 0.8978 (t0) cc_final: 0.8734 (t0) REVERT: B 206 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7432 (mttp) REVERT: B 247 SER cc_start: 0.8492 (t) cc_final: 0.8165 (m) REVERT: B 261 ASN cc_start: 0.7630 (p0) cc_final: 0.7098 (t0) REVERT: B 303 MET cc_start: 0.8944 (mmt) cc_final: 0.8686 (mmt) REVERT: B 415 LEU cc_start: 0.7469 (tt) cc_final: 0.7200 (tm) REVERT: B 420 PHE cc_start: 0.7374 (m-10) cc_final: 0.7077 (t80) REVERT: C 24 MET cc_start: 0.8330 (ptt) cc_final: 0.7100 (ptt) REVERT: C 41 ASP cc_start: 0.8943 (t0) cc_final: 0.8636 (t0) REVERT: C 85 ASN cc_start: 0.8953 (t0) cc_final: 0.8751 (t0) REVERT: C 126 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 210 ASP cc_start: 0.7866 (m-30) cc_final: 0.7607 (m-30) REVERT: C 227 GLU cc_start: 0.8624 (pt0) cc_final: 0.8407 (pt0) REVERT: C 233 GLU cc_start: 0.6819 (tt0) cc_final: 0.6342 (mt-10) REVERT: C 261 ASN cc_start: 0.7555 (p0) cc_final: 0.7107 (t0) REVERT: C 316 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6448 (tm-30) REVERT: C 415 LEU cc_start: 0.7517 (tt) cc_final: 0.7293 (tm) REVERT: C 420 PHE cc_start: 0.7428 (m-10) cc_final: 0.7188 (t80) REVERT: D 24 MET cc_start: 0.8396 (ptt) cc_final: 0.7806 (ptt) REVERT: D 45 ARG cc_start: 0.8998 (ptt90) cc_final: 0.8704 (ptt-90) REVERT: D 72 MET cc_start: 0.8662 (mtm) cc_final: 0.8422 (mtt) REVERT: D 85 ASN cc_start: 0.8993 (t0) cc_final: 0.8718 (t0) REVERT: D 206 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7687 (mttp) REVERT: D 210 ASP cc_start: 0.7807 (m-30) cc_final: 0.7576 (m-30) REVERT: D 227 GLU cc_start: 0.8635 (pt0) cc_final: 0.8429 (pt0) REVERT: D 261 ASN cc_start: 0.7497 (p0) cc_final: 0.7002 (t0) REVERT: D 415 LEU cc_start: 0.7496 (tt) cc_final: 0.7270 (tm) REVERT: E 24 MET cc_start: 0.8228 (ptt) cc_final: 0.6812 (ptt) REVERT: E 102 ASP cc_start: 0.8212 (t0) cc_final: 0.7966 (t70) REVERT: E 104 SER cc_start: 0.8910 (t) cc_final: 0.8658 (p) REVERT: E 206 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7687 (mttp) REVERT: E 261 ASN cc_start: 0.7537 (p0) cc_final: 0.7170 (t0) REVERT: E 420 PHE cc_start: 0.7374 (m-10) cc_final: 0.7076 (t80) outliers start: 0 outliers final: 1 residues processed: 463 average time/residue: 1.1428 time to fit residues: 582.0649 Evaluate side-chains 260 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 51 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.3842 ------------------------------------------------------------------------------- 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 B 62 ASN B 82 GLN B 231 HIS C 62 ASN C 123 ASN C 418 ASN D 62 ASN D 418 ASN E 62 ASN E 123 ASN E 418 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14505 Z= 0.277 Angle : 0.686 8.048 19685 Z= 0.345 Chirality : 0.047 0.184 2260 Planarity : 0.005 0.045 2430 Dihedral : 11.295 73.045 2197 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.07 % Allowed : 14.23 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.17), residues: 1710 helix: -3.51 (0.14), residues: 630 sheet: -1.20 (0.25), residues: 370 loop : -2.15 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 110 HIS 0.002 0.001 HIS B 231 PHE 0.020 0.002 PHE D 322 TYR 0.012 0.002 TYR A 144 ARG 0.004 0.000 ARG D 229 *********************** 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 384 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 322 time to evaluate : 1.836 Fit side-chains REVERT: A 102 ASP cc_start: 0.8281 (t70) cc_final: 0.7997 (t70) REVERT: A 126 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 206 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7539 (mmtm) REVERT: A 210 ASP cc_start: 0.7696 (m-30) cc_final: 0.7413 (m-30) REVERT: A 235 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7345 (mm-40) REVERT: A 303 MET cc_start: 0.8990 (mmt) cc_final: 0.8690 (mmt) REVERT: A 415 LEU cc_start: 0.7258 (tt) cc_final: 0.6993 (tm) REVERT: A 420 PHE cc_start: 0.7262 (m-10) cc_final: 0.6995 (t80) REVERT: B 102 ASP cc_start: 0.8196 (t70) cc_final: 0.7923 (t70) REVERT: B 206 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7313 (mttp) REVERT: B 210 ASP cc_start: 0.7782 (m-30) cc_final: 0.7292 (m-30) REVERT: B 235 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7879 (mm-40) REVERT: B 247 SER cc_start: 0.8498 (t) cc_final: 0.8204 (m) REVERT: B 415 LEU cc_start: 0.7279 (tt) cc_final: 0.7066 (tm) REVERT: B 420 PHE cc_start: 0.7462 (m-10) cc_final: 0.7089 (t80) REVERT: C 28 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7389 (mm-30) REVERT: C 36 LYS cc_start: 0.7829 (tppt) cc_final: 0.7497 (tptm) REVERT: C 102 ASP cc_start: 0.8246 (t70) cc_final: 0.7967 (t70) REVERT: C 126 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7386 (mt-10) REVERT: C 206 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7397 (mttp) REVERT: C 210 ASP cc_start: 0.7795 (m-30) cc_final: 0.7486 (m-30) REVERT: C 235 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7365 (mt0) REVERT: C 261 ASN cc_start: 0.7903 (p0) cc_final: 0.7262 (t0) REVERT: C 303 MET cc_start: 0.8998 (mmt) cc_final: 0.8424 (mmt) REVERT: C 415 LEU cc_start: 0.7176 (tt) cc_final: 0.6879 (tm) REVERT: C 420 PHE cc_start: 0.7465 (m-10) cc_final: 0.7160 (t80) REVERT: D 85 ASN cc_start: 0.9017 (t0) cc_final: 0.8754 (t0) REVERT: D 102 ASP cc_start: 0.8187 (t70) cc_final: 0.7792 (t70) REVERT: D 126 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 164 ASP cc_start: 0.8939 (p0) cc_final: 0.8671 (p0) REVERT: D 206 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7649 (mttp) REVERT: D 210 ASP cc_start: 0.7753 (m-30) cc_final: 0.7512 (m-30) REVERT: D 235 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7604 (mt0) REVERT: D 415 LEU cc_start: 0.7327 (tt) cc_final: 0.6968 (tm) REVERT: E 24 MET cc_start: 0.7775 (ptt) cc_final: 0.7425 (ptt) REVERT: E 28 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7288 (mm-30) REVERT: E 94 TYR cc_start: 0.8005 (t80) cc_final: 0.7645 (t80) REVERT: E 107 ASP cc_start: 0.8375 (m-30) cc_final: 0.8097 (m-30) REVERT: E 164 ASP cc_start: 0.9055 (p0) cc_final: 0.8798 (p0) REVERT: E 206 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7505 (mttp) REVERT: E 235 GLN cc_start: 0.8009 (mm110) cc_final: 0.7793 (mm-40) REVERT: E 398 ARG cc_start: 0.6689 (ttm170) cc_final: 0.6444 (ttm170) REVERT: E 420 PHE cc_start: 0.7338 (m-10) cc_final: 0.7080 (t80) outliers start: 62 outliers final: 27 residues processed: 355 average time/residue: 0.9839 time to fit residues: 389.9922 Evaluate side-chains 294 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 154 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 0.2980 chunk 153 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 180 ASN B 418 ASN C 82 GLN D 82 GLN E 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14505 Z= 0.170 Angle : 0.597 7.991 19685 Z= 0.293 Chirality : 0.045 0.178 2260 Planarity : 0.004 0.030 2430 Dihedral : 7.889 45.778 2197 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.41 % Allowed : 16.98 % Favored : 79.61 % 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: -2.81 (0.18), residues: 1710 helix: -2.46 (0.17), residues: 620 sheet: -0.68 (0.27), residues: 370 loop : -1.77 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.001 0.000 HIS D 231 PHE 0.021 0.001 PHE D 322 TYR 0.011 0.001 TYR D 144 ARG 0.005 0.000 ARG B 268 *********************** 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 361 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 309 time to evaluate : 1.683 Fit side-chains REVERT: A 102 ASP cc_start: 0.8210 (t70) cc_final: 0.7968 (t70) REVERT: A 126 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 206 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7411 (mmtm) REVERT: A 210 ASP cc_start: 0.7661 (m-30) cc_final: 0.7330 (m-30) REVERT: A 235 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 303 MET cc_start: 0.8910 (mmt) cc_final: 0.8628 (mmt) REVERT: A 415 LEU cc_start: 0.7150 (tt) cc_final: 0.6921 (tm) REVERT: A 420 PHE cc_start: 0.7260 (m-10) cc_final: 0.6928 (t80) REVERT: B 24 MET cc_start: 0.8061 (ptt) cc_final: 0.7565 (ptp) REVERT: B 28 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7402 (mm-30) REVERT: B 41 ASP cc_start: 0.8818 (t0) cc_final: 0.8563 (t0) REVERT: B 62 ASN cc_start: 0.8478 (m-40) cc_final: 0.8071 (m110) REVERT: B 102 ASP cc_start: 0.8128 (t70) cc_final: 0.7835 (t70) REVERT: B 130 ASP cc_start: 0.7794 (m-30) cc_final: 0.7513 (t0) REVERT: B 160 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7238 (p0) REVERT: B 164 ASP cc_start: 0.8956 (p0) cc_final: 0.8635 (p0) REVERT: B 206 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7428 (mttp) REVERT: B 210 ASP cc_start: 0.7772 (m-30) cc_final: 0.7285 (m-30) REVERT: C 28 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7264 (mm-30) REVERT: C 36 LYS cc_start: 0.7870 (tppt) cc_final: 0.7585 (tptm) REVERT: C 102 ASP cc_start: 0.8220 (t70) cc_final: 0.7926 (t70) REVERT: C 126 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7344 (mt-10) REVERT: C 206 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7371 (mttp) REVERT: C 210 ASP cc_start: 0.7753 (m-30) cc_final: 0.7448 (m-30) REVERT: C 303 MET cc_start: 0.8969 (mmt) cc_final: 0.8341 (mmt) REVERT: C 415 LEU cc_start: 0.7123 (tt) cc_final: 0.6808 (tm) REVERT: D 62 ASN cc_start: 0.8493 (m-40) cc_final: 0.8226 (m-40) REVERT: D 85 ASN cc_start: 0.9002 (t0) cc_final: 0.8783 (t0) REVERT: D 102 ASP cc_start: 0.8165 (t70) cc_final: 0.7739 (t70) REVERT: D 126 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: D 206 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7585 (mttp) REVERT: D 210 ASP cc_start: 0.7707 (m-30) cc_final: 0.7431 (m-30) REVERT: D 235 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7573 (mt0) REVERT: D 415 LEU cc_start: 0.7248 (tt) cc_final: 0.6935 (tm) REVERT: E 24 MET cc_start: 0.7658 (ptt) cc_final: 0.7412 (ptt) REVERT: E 62 ASN cc_start: 0.8462 (m-40) cc_final: 0.8214 (m-40) REVERT: E 94 TYR cc_start: 0.8008 (t80) cc_final: 0.7712 (t80) REVERT: E 102 ASP cc_start: 0.8039 (t70) cc_final: 0.7653 (t70) REVERT: E 107 ASP cc_start: 0.8403 (m-30) cc_final: 0.8117 (m-30) REVERT: E 130 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7320 (t0) REVERT: E 173 GLU cc_start: 0.8151 (tt0) cc_final: 0.7930 (tt0) REVERT: E 206 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7540 (mttp) REVERT: E 235 GLN cc_start: 0.7980 (mm110) cc_final: 0.7386 (mt0) REVERT: E 398 ARG cc_start: 0.6681 (ttm170) cc_final: 0.6372 (mmm-85) REVERT: E 420 PHE cc_start: 0.7371 (m-10) cc_final: 0.7128 (t80) outliers start: 52 outliers final: 16 residues processed: 337 average time/residue: 0.8387 time to fit residues: 317.6746 Evaluate side-chains 314 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 295 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 155 optimal weight: 0.0980 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 58 ASN C 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14505 Z= 0.160 Angle : 0.569 7.383 19685 Z= 0.278 Chirality : 0.044 0.171 2260 Planarity : 0.003 0.033 2430 Dihedral : 5.915 34.534 2197 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.61 % Allowed : 17.77 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.19), residues: 1710 helix: -1.75 (0.19), residues: 620 sheet: 0.41 (0.30), residues: 315 loop : -1.49 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.001 0.000 HIS B 231 PHE 0.022 0.001 PHE D 322 TYR 0.010 0.001 TYR E 144 ARG 0.003 0.000 ARG B 268 *********************** 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 351 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 296 time to evaluate : 1.550 Fit side-chains REVERT: A 24 MET cc_start: 0.7846 (ptt) cc_final: 0.7596 (ptm) REVERT: A 32 LYS cc_start: 0.7819 (tttt) cc_final: 0.7334 (ttpt) REVERT: A 36 LYS cc_start: 0.8003 (tptt) cc_final: 0.7531 (tptm) REVERT: A 102 ASP cc_start: 0.8310 (t70) cc_final: 0.7942 (t70) REVERT: A 126 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7223 (mt-10) REVERT: A 206 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7681 (mttp) REVERT: A 210 ASP cc_start: 0.7647 (m-30) cc_final: 0.7339 (m-30) REVERT: A 235 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7346 (mm-40) REVERT: A 279 MET cc_start: 0.7601 (tpt) cc_final: 0.7197 (tpt) REVERT: A 303 MET cc_start: 0.8920 (mmt) cc_final: 0.8615 (mmt) REVERT: A 420 PHE cc_start: 0.7290 (m-10) cc_final: 0.6930 (t80) REVERT: B 24 MET cc_start: 0.7933 (ptt) cc_final: 0.7429 (ptp) REVERT: B 28 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7376 (mm-30) REVERT: B 62 ASN cc_start: 0.8412 (m-40) cc_final: 0.8207 (m110) REVERT: B 102 ASP cc_start: 0.8165 (t70) cc_final: 0.7795 (t70) REVERT: B 130 ASP cc_start: 0.7746 (m-30) cc_final: 0.7519 (t0) REVERT: B 206 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7433 (mttp) REVERT: B 210 ASP cc_start: 0.7724 (m-30) cc_final: 0.7222 (m-30) REVERT: B 235 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7280 (mt0) REVERT: B 423 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 28 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7432 (mm-30) REVERT: C 36 LYS cc_start: 0.7891 (tppt) cc_final: 0.7585 (tptm) REVERT: C 102 ASP cc_start: 0.8225 (t70) cc_final: 0.7900 (t70) REVERT: C 126 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7340 (mt-10) REVERT: C 171 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8448 (mt0) REVERT: C 206 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7371 (mttp) REVERT: C 210 ASP cc_start: 0.7735 (m-30) cc_final: 0.7424 (m-30) REVERT: C 235 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7824 (mm-40) REVERT: C 279 MET cc_start: 0.7825 (tpt) cc_final: 0.7507 (tpt) REVERT: C 303 MET cc_start: 0.8964 (mmt) cc_final: 0.8332 (mmt) REVERT: D 62 ASN cc_start: 0.8477 (m-40) cc_final: 0.8125 (m-40) REVERT: D 85 ASN cc_start: 0.8983 (t0) cc_final: 0.8759 (t0) REVERT: D 102 ASP cc_start: 0.8140 (t70) cc_final: 0.7724 (t70) REVERT: D 160 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7308 (OUTLIER) REVERT: D 164 ASP cc_start: 0.8912 (p0) cc_final: 0.8626 (p0) REVERT: D 206 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7583 (mttp) REVERT: D 210 ASP cc_start: 0.7681 (m-30) cc_final: 0.7407 (m-30) REVERT: D 235 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7622 (mt0) REVERT: D 398 ARG cc_start: 0.6614 (ttm170) cc_final: 0.6298 (mmm-85) REVERT: D 423 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8407 (mp) REVERT: E 62 ASN cc_start: 0.8440 (m-40) cc_final: 0.8223 (m-40) REVERT: E 102 ASP cc_start: 0.8131 (t70) cc_final: 0.7708 (t70) REVERT: E 130 ASP cc_start: 0.7748 (m-30) cc_final: 0.7531 (t0) REVERT: E 164 ASP cc_start: 0.9059 (p0) cc_final: 0.8755 (p0) REVERT: E 171 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: E 206 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7508 (mttp) REVERT: E 235 GLN cc_start: 0.7859 (mm110) cc_final: 0.7242 (mt0) REVERT: E 398 ARG cc_start: 0.6604 (ttm170) cc_final: 0.6391 (mmm-85) REVERT: E 420 PHE cc_start: 0.7374 (m-10) cc_final: 0.7122 (t80) outliers start: 55 outliers final: 22 residues processed: 329 average time/residue: 0.9798 time to fit residues: 361.0778 Evaluate side-chains 300 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14505 Z= 0.265 Angle : 0.595 6.748 19685 Z= 0.296 Chirality : 0.046 0.181 2260 Planarity : 0.004 0.033 2430 Dihedral : 5.218 23.360 2197 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.98 % Allowed : 17.31 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.20), residues: 1710 helix: -1.08 (0.21), residues: 580 sheet: 0.33 (0.30), residues: 325 loop : -1.05 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 302 HIS 0.002 0.001 HIS C 125 PHE 0.027 0.002 PHE C 322 TYR 0.013 0.001 TYR A 144 ARG 0.003 0.000 ARG E 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 362 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 286 time to evaluate : 1.658 Fit side-chains REVERT: A 32 LYS cc_start: 0.7848 (tttt) cc_final: 0.7388 (ttpt) REVERT: A 36 LYS cc_start: 0.8053 (tptt) cc_final: 0.7634 (tptm) REVERT: A 102 ASP cc_start: 0.8317 (t70) cc_final: 0.7972 (t70) REVERT: A 126 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7246 (mt-10) REVERT: A 206 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7638 (mttp) REVERT: A 210 ASP cc_start: 0.7677 (m-30) cc_final: 0.7401 (m-30) REVERT: A 235 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7370 (mm-40) REVERT: A 279 MET cc_start: 0.7531 (tpt) cc_final: 0.7239 (tpt) REVERT: A 415 LEU cc_start: 0.7235 (tt) cc_final: 0.6927 (tm) REVERT: A 420 PHE cc_start: 0.7358 (m-10) cc_final: 0.6958 (t80) REVERT: B 24 MET cc_start: 0.7711 (ptt) cc_final: 0.6923 (ptp) REVERT: B 28 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 62 ASN cc_start: 0.8485 (m-40) cc_final: 0.8139 (m110) REVERT: B 102 ASP cc_start: 0.8146 (t70) cc_final: 0.7832 (t70) REVERT: B 130 ASP cc_start: 0.7875 (m-30) cc_final: 0.7586 (t0) REVERT: B 206 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7393 (mttp) REVERT: B 210 ASP cc_start: 0.7711 (m-30) cc_final: 0.7143 (m-30) REVERT: B 323 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6739 (mp) REVERT: B 424 THR cc_start: 0.8583 (m) cc_final: 0.8336 (m) REVERT: C 28 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7452 (mm-30) REVERT: C 36 LYS cc_start: 0.7997 (tppt) cc_final: 0.7670 (tptm) REVERT: C 126 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 169 ILE cc_start: 0.8879 (pt) cc_final: 0.8676 (pt) REVERT: C 206 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7395 (mttp) REVERT: C 210 ASP cc_start: 0.7736 (m-30) cc_final: 0.7414 (m-30) REVERT: C 415 LEU cc_start: 0.7192 (tt) cc_final: 0.6834 (tm) REVERT: D 32 LYS cc_start: 0.7676 (tttm) cc_final: 0.7370 (ttpt) REVERT: D 62 ASN cc_start: 0.8502 (m-40) cc_final: 0.8157 (m-40) REVERT: D 85 ASN cc_start: 0.9011 (t0) cc_final: 0.8756 (t0) REVERT: D 102 ASP cc_start: 0.8237 (t70) cc_final: 0.7832 (t70) REVERT: D 130 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7634 (t0) REVERT: D 206 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7643 (mttp) REVERT: D 235 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7638 (mt0) REVERT: D 398 ARG cc_start: 0.6665 (ttm170) cc_final: 0.6321 (mmm-85) REVERT: D 415 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6907 (tm) REVERT: D 420 PHE cc_start: 0.7584 (m-10) cc_final: 0.7255 (t80) REVERT: E 24 MET cc_start: 0.7475 (ptt) cc_final: 0.7066 (ptp) REVERT: E 28 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6833 (mm-30) REVERT: E 62 ASN cc_start: 0.8509 (m-40) cc_final: 0.8273 (m-40) REVERT: E 102 ASP cc_start: 0.8133 (t70) cc_final: 0.7826 (t70) REVERT: E 130 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7467 (t0) REVERT: E 206 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7496 (mttp) REVERT: E 398 ARG cc_start: 0.6652 (ttm170) cc_final: 0.6408 (mmm-85) REVERT: E 420 PHE cc_start: 0.7393 (m-10) cc_final: 0.7087 (t80) outliers start: 76 outliers final: 40 residues processed: 328 average time/residue: 0.9682 time to fit residues: 356.1787 Evaluate side-chains 308 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 199 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14505 Z= 0.218 Angle : 0.573 8.302 19685 Z= 0.284 Chirality : 0.045 0.165 2260 Planarity : 0.003 0.032 2430 Dihedral : 4.952 22.942 2197 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.79 % Allowed : 17.38 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1710 helix: -0.76 (0.22), residues: 580 sheet: 0.38 (0.30), residues: 325 loop : -0.94 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.002 0.000 HIS B 231 PHE 0.029 0.002 PHE C 322 TYR 0.011 0.001 TYR D 144 ARG 0.003 0.000 ARG B 43 *********************** 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 359 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 286 time to evaluate : 1.595 Fit side-chains REVERT: A 32 LYS cc_start: 0.7803 (tttt) cc_final: 0.7360 (ttpt) REVERT: A 36 LYS cc_start: 0.8069 (tptt) cc_final: 0.7672 (tptm) REVERT: A 126 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 206 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7630 (mttp) REVERT: A 210 ASP cc_start: 0.7700 (m-30) cc_final: 0.7439 (m-30) REVERT: A 235 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7349 (mm-40) REVERT: A 262 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6732 (ptm) REVERT: A 303 MET cc_start: 0.8986 (mmt) cc_final: 0.8769 (mmt) REVERT: A 420 PHE cc_start: 0.7358 (m-10) cc_final: 0.6969 (t80) REVERT: A 423 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 24 MET cc_start: 0.7484 (ptt) cc_final: 0.6825 (ptp) REVERT: B 28 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 62 ASN cc_start: 0.8452 (m-40) cc_final: 0.8221 (m110) REVERT: B 102 ASP cc_start: 0.8145 (t70) cc_final: 0.7788 (t70) REVERT: B 130 ASP cc_start: 0.7897 (m-30) cc_final: 0.7622 (t0) REVERT: B 206 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7312 (mttp) REVERT: B 210 ASP cc_start: 0.7680 (m-30) cc_final: 0.7123 (m-30) REVERT: B 235 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7741 (mm-40) REVERT: B 315 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6949 (mp) REVERT: B 415 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6997 (tm) REVERT: B 424 THR cc_start: 0.8612 (m) cc_final: 0.8397 (m) REVERT: C 28 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7551 (mm-30) REVERT: C 36 LYS cc_start: 0.8017 (tppt) cc_final: 0.7717 (tptm) REVERT: C 101 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8175 (tt) REVERT: C 102 ASP cc_start: 0.8293 (t70) cc_final: 0.7802 (t70) REVERT: C 126 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 169 ILE cc_start: 0.8899 (pt) cc_final: 0.8688 (pt) REVERT: C 171 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: C 206 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7374 (mttp) REVERT: C 210 ASP cc_start: 0.7691 (m-30) cc_final: 0.7404 (m-30) REVERT: C 279 MET cc_start: 0.7903 (tpt) cc_final: 0.7597 (tpt) REVERT: C 303 MET cc_start: 0.8968 (mmt) cc_final: 0.8431 (mmt) REVERT: C 398 ARG cc_start: 0.6521 (ttm170) cc_final: 0.6167 (mmm-85) REVERT: C 415 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6791 (tm) REVERT: D 32 LYS cc_start: 0.7715 (tttm) cc_final: 0.7434 (ttpt) REVERT: D 62 ASN cc_start: 0.8482 (m-40) cc_final: 0.8131 (m-40) REVERT: D 85 ASN cc_start: 0.9030 (t0) cc_final: 0.8782 (t0) REVERT: D 102 ASP cc_start: 0.8226 (t70) cc_final: 0.7797 (t70) REVERT: D 206 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7620 (mttm) REVERT: D 235 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7676 (mt0) REVERT: D 398 ARG cc_start: 0.6627 (ttm170) cc_final: 0.6319 (mmm-85) REVERT: D 415 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6892 (tm) REVERT: D 420 PHE cc_start: 0.7613 (m-10) cc_final: 0.7257 (t80) REVERT: E 62 ASN cc_start: 0.8494 (m-40) cc_final: 0.8261 (m-40) REVERT: E 97 ASP cc_start: 0.7789 (m-30) cc_final: 0.7344 (t0) REVERT: E 102 ASP cc_start: 0.8200 (t70) cc_final: 0.7855 (t70) REVERT: E 130 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7414 (t0) REVERT: E 206 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7463 (mttp) REVERT: E 235 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7324 (mt0) REVERT: E 398 ARG cc_start: 0.6629 (ttm170) cc_final: 0.6416 (mmm-85) REVERT: E 420 PHE cc_start: 0.7342 (m-10) cc_final: 0.7014 (t80) outliers start: 73 outliers final: 36 residues processed: 327 average time/residue: 0.9479 time to fit residues: 347.3908 Evaluate side-chains 314 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 219 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 256 VAL 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: 2.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 D 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14505 Z= 0.317 Angle : 0.619 8.906 19685 Z= 0.309 Chirality : 0.046 0.170 2260 Planarity : 0.004 0.033 2430 Dihedral : 5.011 24.672 2197 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.79 % Allowed : 18.69 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1710 helix: -0.64 (0.22), residues: 585 sheet: 0.53 (0.31), residues: 325 loop : -0.92 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 302 HIS 0.002 0.001 HIS B 231 PHE 0.028 0.002 PHE A 322 TYR 0.012 0.002 TYR D 144 ARG 0.003 0.000 ARG E 135 *********************** 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 354 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 281 time to evaluate : 1.526 Fit side-chains REVERT: A 32 LYS cc_start: 0.7810 (tttt) cc_final: 0.7354 (ttpt) REVERT: A 36 LYS cc_start: 0.8072 (tptt) cc_final: 0.7650 (tptm) REVERT: A 102 ASP cc_start: 0.8314 (t70) cc_final: 0.7925 (t70) REVERT: A 126 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 206 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7380 (mmtm) REVERT: A 210 ASP cc_start: 0.7752 (m-30) cc_final: 0.7480 (m-30) REVERT: A 235 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7326 (mm-40) REVERT: A 262 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6630 (ptt) REVERT: A 303 MET cc_start: 0.8996 (mmt) cc_final: 0.8779 (mmt) REVERT: A 415 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6881 (tm) REVERT: A 420 PHE cc_start: 0.7382 (m-10) cc_final: 0.6986 (t80) REVERT: B 62 ASN cc_start: 0.8551 (m-40) cc_final: 0.8203 (m110) REVERT: B 69 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: B 102 ASP cc_start: 0.8181 (t70) cc_final: 0.7818 (t70) REVERT: B 130 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7735 (t0) REVERT: B 206 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7270 (mttm) REVERT: B 210 ASP cc_start: 0.7705 (m-30) cc_final: 0.7125 (m-30) REVERT: B 235 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7750 (mm-40) REVERT: B 315 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6963 (mp) REVERT: B 415 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6958 (tm) REVERT: B 424 THR cc_start: 0.8615 (m) cc_final: 0.8366 (m) REVERT: C 28 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7542 (mm-30) REVERT: C 32 LYS cc_start: 0.7783 (tttm) cc_final: 0.7407 (ttpt) REVERT: C 36 LYS cc_start: 0.8045 (tppt) cc_final: 0.7773 (tptm) REVERT: C 126 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 169 ILE cc_start: 0.8890 (pt) cc_final: 0.8681 (pt) REVERT: C 206 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7417 (mttp) REVERT: C 210 ASP cc_start: 0.7679 (m-30) cc_final: 0.7294 (m-30) REVERT: C 279 MET cc_start: 0.7953 (tpt) cc_final: 0.7609 (tpt) REVERT: C 303 MET cc_start: 0.8985 (mmt) cc_final: 0.8411 (mmt) REVERT: C 398 ARG cc_start: 0.6526 (ttm170) cc_final: 0.6170 (mmm-85) REVERT: C 415 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6764 (tm) REVERT: D 62 ASN cc_start: 0.8540 (m-40) cc_final: 0.8196 (m-40) REVERT: D 85 ASN cc_start: 0.9039 (t0) cc_final: 0.8786 (t0) REVERT: D 102 ASP cc_start: 0.8308 (t70) cc_final: 0.7951 (t70) REVERT: D 160 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7444 (OUTLIER) REVERT: D 164 ASP cc_start: 0.8891 (p0) cc_final: 0.8646 (p0) REVERT: D 206 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7646 (mttp) REVERT: D 235 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7645 (mt0) REVERT: D 398 ARG cc_start: 0.6617 (ttm170) cc_final: 0.6284 (mmm-85) REVERT: D 415 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6829 (tm) REVERT: E 24 MET cc_start: 0.7278 (ptp) cc_final: 0.6980 (ptp) REVERT: E 62 ASN cc_start: 0.8571 (m-40) cc_final: 0.8351 (m110) REVERT: E 102 ASP cc_start: 0.8290 (t70) cc_final: 0.7940 (t70) REVERT: E 130 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7604 (t0) REVERT: E 206 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7494 (mttp) REVERT: E 235 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7293 (mt0) REVERT: E 420 PHE cc_start: 0.7374 (m-10) cc_final: 0.7045 (t80) outliers start: 73 outliers final: 52 residues processed: 326 average time/residue: 0.9601 time to fit residues: 351.1508 Evaluate side-chains 322 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 261 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 199 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14505 Z= 0.259 Angle : 0.593 8.227 19685 Z= 0.295 Chirality : 0.045 0.165 2260 Planarity : 0.004 0.032 2430 Dihedral : 4.951 25.150 2197 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.72 % Allowed : 19.41 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1710 helix: -0.49 (0.22), residues: 585 sheet: 0.56 (0.31), residues: 325 loop : -0.84 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 259 HIS 0.002 0.000 HIS B 231 PHE 0.028 0.002 PHE C 322 TYR 0.010 0.001 TYR D 144 ARG 0.009 0.000 ARG E 398 *********************** 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 336 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 264 time to evaluate : 1.798 Fit side-chains REVERT: A 32 LYS cc_start: 0.7775 (tttt) cc_final: 0.7421 (ttpt) REVERT: A 36 LYS cc_start: 0.8064 (tptt) cc_final: 0.7645 (tptm) REVERT: A 102 ASP cc_start: 0.8350 (t70) cc_final: 0.7969 (t70) REVERT: A 105 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7804 (mtt) REVERT: A 126 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 206 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7388 (mmtm) REVERT: A 210 ASP cc_start: 0.7740 (m-30) cc_final: 0.7450 (m-30) REVERT: A 262 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6650 (ptt) REVERT: A 303 MET cc_start: 0.8999 (mmt) cc_final: 0.8789 (mmt) REVERT: A 415 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6865 (tm) REVERT: A 420 PHE cc_start: 0.7385 (m-10) cc_final: 0.6996 (t80) REVERT: B 62 ASN cc_start: 0.8518 (m-40) cc_final: 0.8165 (m110) REVERT: B 69 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: B 102 ASP cc_start: 0.8067 (t70) cc_final: 0.7766 (t70) REVERT: B 107 ASP cc_start: 0.8366 (m-30) cc_final: 0.8057 (m-30) REVERT: B 130 ASP cc_start: 0.8034 (m-30) cc_final: 0.7744 (t0) REVERT: B 206 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7259 (mttm) REVERT: B 210 ASP cc_start: 0.7656 (m-30) cc_final: 0.7109 (m-30) REVERT: B 235 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7746 (mm-40) REVERT: B 262 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6439 (ptt) REVERT: B 315 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6934 (mp) REVERT: B 415 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6953 (tm) REVERT: B 424 THR cc_start: 0.8608 (m) cc_final: 0.8357 (m) REVERT: C 28 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7562 (mm-30) REVERT: C 32 LYS cc_start: 0.7762 (tttm) cc_final: 0.7387 (ttpt) REVERT: C 36 LYS cc_start: 0.8015 (tppt) cc_final: 0.7770 (tptm) REVERT: C 101 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8212 (tt) REVERT: C 102 ASP cc_start: 0.8340 (t70) cc_final: 0.7808 (t70) REVERT: C 126 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7418 (mt-10) REVERT: C 169 ILE cc_start: 0.8885 (pt) cc_final: 0.8676 (pt) REVERT: C 206 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7406 (mttp) REVERT: C 210 ASP cc_start: 0.7652 (m-30) cc_final: 0.7355 (m-30) REVERT: C 279 MET cc_start: 0.7921 (tpt) cc_final: 0.7606 (tpt) REVERT: C 303 MET cc_start: 0.8960 (mmt) cc_final: 0.8414 (mmt) REVERT: C 398 ARG cc_start: 0.6489 (ttm170) cc_final: 0.6152 (mmm-85) REVERT: C 415 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6758 (tm) REVERT: D 62 ASN cc_start: 0.8512 (m-40) cc_final: 0.8162 (m-40) REVERT: D 85 ASN cc_start: 0.9039 (t0) cc_final: 0.8790 (t0) REVERT: D 102 ASP cc_start: 0.8278 (t70) cc_final: 0.7898 (t70) REVERT: D 206 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7650 (mttp) REVERT: D 235 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7683 (mt0) REVERT: D 398 ARG cc_start: 0.6593 (ttm170) cc_final: 0.6286 (mmm-85) REVERT: D 415 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6828 (tm) REVERT: E 24 MET cc_start: 0.7227 (ptp) cc_final: 0.6842 (ptp) REVERT: E 62 ASN cc_start: 0.8565 (m-40) cc_final: 0.8358 (m110) REVERT: E 102 ASP cc_start: 0.8291 (t70) cc_final: 0.7962 (t70) REVERT: E 130 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7615 (t0) REVERT: E 206 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7458 (mttp) REVERT: E 235 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7283 (mt0) REVERT: E 398 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.6555 (ttm170) REVERT: E 420 PHE cc_start: 0.7366 (m-10) cc_final: 0.7036 (t80) outliers start: 72 outliers final: 51 residues processed: 311 average time/residue: 0.9593 time to fit residues: 335.6278 Evaluate side-chains 328 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 266 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 56 THR 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 199 THR Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.8980 chunk 143 optimal weight: 0.0970 chunk 152 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 161 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14505 Z= 0.144 Angle : 0.541 8.158 19685 Z= 0.269 Chirality : 0.043 0.169 2260 Planarity : 0.003 0.032 2430 Dihedral : 4.662 22.745 2197 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.54 % Allowed : 20.66 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1710 helix: -0.08 (0.23), residues: 585 sheet: 0.15 (0.29), residues: 350 loop : -0.85 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.001 0.000 HIS C 125 PHE 0.028 0.001 PHE E 322 TYR 0.008 0.001 TYR D 144 ARG 0.006 0.000 ARG E 398 *********************** 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 328 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 274 time to evaluate : 1.742 Fit side-chains REVERT: A 32 LYS cc_start: 0.7744 (tttt) cc_final: 0.7392 (ttpt) REVERT: A 36 LYS cc_start: 0.8056 (tptt) cc_final: 0.7643 (tptm) REVERT: A 102 ASP cc_start: 0.8317 (t70) cc_final: 0.7999 (t70) REVERT: A 105 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7805 (mtt) REVERT: A 126 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 206 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7393 (mmtm) REVERT: A 210 ASP cc_start: 0.7682 (m-30) cc_final: 0.7387 (m-30) REVERT: A 262 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6593 (ptt) REVERT: A 415 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6864 (tm) REVERT: A 420 PHE cc_start: 0.7353 (m-10) cc_final: 0.6949 (t80) REVERT: B 102 ASP cc_start: 0.8063 (t70) cc_final: 0.7734 (t70) REVERT: B 107 ASP cc_start: 0.8333 (m-30) cc_final: 0.8030 (m-30) REVERT: B 130 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7647 (t0) REVERT: B 206 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7454 (mttp) REVERT: B 262 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6521 (ptt) REVERT: B 315 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6959 (mp) REVERT: B 415 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6820 (tm) REVERT: C 28 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 32 LYS cc_start: 0.7815 (tttm) cc_final: 0.7445 (ttpt) REVERT: C 36 LYS cc_start: 0.7984 (tppt) cc_final: 0.7735 (tptm) REVERT: C 102 ASP cc_start: 0.8315 (t70) cc_final: 0.7735 (t70) REVERT: C 126 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 130 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7856 (t0) REVERT: C 169 ILE cc_start: 0.8935 (pt) cc_final: 0.8728 (pt) REVERT: C 206 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7366 (mttp) REVERT: C 210 ASP cc_start: 0.7643 (m-30) cc_final: 0.7293 (m-30) REVERT: C 279 MET cc_start: 0.7868 (tpt) cc_final: 0.7552 (tpt) REVERT: C 303 MET cc_start: 0.8915 (mmt) cc_final: 0.8411 (mmt) REVERT: C 398 ARG cc_start: 0.6405 (ttm170) cc_final: 0.6067 (mmm-85) REVERT: C 415 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6702 (tm) REVERT: D 62 ASN cc_start: 0.8392 (m-40) cc_final: 0.8031 (m-40) REVERT: D 85 ASN cc_start: 0.9030 (t0) cc_final: 0.8809 (t0) REVERT: D 102 ASP cc_start: 0.8239 (t70) cc_final: 0.7842 (t70) REVERT: D 206 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7610 (mttp) REVERT: D 235 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7703 (mt0) REVERT: D 398 ARG cc_start: 0.6565 (ttm170) cc_final: 0.6277 (mmm-85) REVERT: D 415 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6858 (tm) REVERT: E 24 MET cc_start: 0.7162 (ptp) cc_final: 0.6892 (ptp) REVERT: E 62 ASN cc_start: 0.8468 (m-40) cc_final: 0.8238 (m-40) REVERT: E 97 ASP cc_start: 0.7806 (m-30) cc_final: 0.7436 (t0) REVERT: E 102 ASP cc_start: 0.8249 (t70) cc_final: 0.7864 (t70) REVERT: E 107 ASP cc_start: 0.8442 (m-30) cc_final: 0.8130 (m-30) REVERT: E 130 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7531 (t0) REVERT: E 206 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7413 (mttp) REVERT: E 235 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7292 (mt0) REVERT: E 279 MET cc_start: 0.7385 (tpt) cc_final: 0.6986 (tpt) REVERT: E 398 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.6480 (ttm170) REVERT: E 420 PHE cc_start: 0.7280 (m-10) cc_final: 0.7026 (t80) outliers start: 54 outliers final: 33 residues processed: 309 average time/residue: 0.9615 time to fit residues: 333.2652 Evaluate side-chains 314 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14505 Z= 0.167 Angle : 0.545 9.144 19685 Z= 0.270 Chirality : 0.044 0.182 2260 Planarity : 0.003 0.032 2430 Dihedral : 4.626 21.118 2197 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.75 % Allowed : 21.84 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1710 helix: 0.08 (0.23), residues: 590 sheet: 0.45 (0.30), residues: 325 loop : -0.75 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS C 125 PHE 0.032 0.001 PHE D 322 TYR 0.010 0.001 TYR C 144 ARG 0.005 0.000 ARG E 398 ********************** 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 315 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 273 time to evaluate : 1.881 Fit side-chains REVERT: A 32 LYS cc_start: 0.7804 (tttt) cc_final: 0.7429 (ttpt) REVERT: A 36 LYS cc_start: 0.8026 (tptt) cc_final: 0.7627 (tptm) REVERT: A 102 ASP cc_start: 0.8299 (t70) cc_final: 0.7956 (t70) REVERT: A 105 MET cc_start: 0.8072 (mtm) cc_final: 0.7796 (mtt) REVERT: A 126 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7282 (mt-10) REVERT: A 206 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7391 (mmtm) REVERT: A 210 ASP cc_start: 0.7692 (m-30) cc_final: 0.7392 (m-30) REVERT: A 262 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6640 (ptt) REVERT: A 415 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6836 (tm) REVERT: A 420 PHE cc_start: 0.7392 (m-10) cc_final: 0.6987 (t80) REVERT: B 102 ASP cc_start: 0.8054 (t70) cc_final: 0.7717 (t70) REVERT: B 107 ASP cc_start: 0.8333 (m-30) cc_final: 0.8026 (m-30) REVERT: B 130 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7658 (t0) REVERT: B 206 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7508 (mttp) REVERT: B 235 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7730 (mm-40) REVERT: B 315 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6982 (mp) REVERT: B 415 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6889 (tm) REVERT: C 32 LYS cc_start: 0.7825 (tttm) cc_final: 0.7447 (ttpt) REVERT: C 36 LYS cc_start: 0.7969 (tppt) cc_final: 0.7730 (tptm) REVERT: C 102 ASP cc_start: 0.8250 (t70) cc_final: 0.7812 (t70) REVERT: C 126 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 130 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7863 (t0) REVERT: C 206 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7408 (mttp) REVERT: C 210 ASP cc_start: 0.7626 (m-30) cc_final: 0.7309 (m-30) REVERT: C 303 MET cc_start: 0.8920 (mmt) cc_final: 0.8370 (mmt) REVERT: C 398 ARG cc_start: 0.6395 (ttm170) cc_final: 0.6081 (mmm-85) REVERT: C 415 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6725 (tm) REVERT: D 62 ASN cc_start: 0.8384 (m-40) cc_final: 0.8019 (m-40) REVERT: D 85 ASN cc_start: 0.9008 (t0) cc_final: 0.8785 (t0) REVERT: D 102 ASP cc_start: 0.8239 (t70) cc_final: 0.7840 (t70) REVERT: D 206 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7615 (mttp) REVERT: D 235 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7705 (mt0) REVERT: D 398 ARG cc_start: 0.6559 (ttm170) cc_final: 0.6256 (mmm-85) REVERT: E 62 ASN cc_start: 0.8455 (m-40) cc_final: 0.8217 (m-40) REVERT: E 102 ASP cc_start: 0.8242 (t70) cc_final: 0.7855 (t70) REVERT: E 130 ASP cc_start: 0.7811 (m-30) cc_final: 0.7582 (t0) REVERT: E 206 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7409 (mttp) REVERT: E 235 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7273 (mt0) REVERT: E 279 MET cc_start: 0.7383 (tpt) cc_final: 0.6994 (tpt) REVERT: E 398 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.6466 (ttm170) outliers start: 42 outliers final: 32 residues processed: 300 average time/residue: 0.9224 time to fit residues: 310.7599 Evaluate side-chains 305 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 266 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 chunk 17 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.130910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.094085 restraints weight = 16731.513| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.67 r_work: 0.2818 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14505 Z= 0.143 Angle : 0.537 7.792 19685 Z= 0.267 Chirality : 0.043 0.171 2260 Planarity : 0.003 0.032 2430 Dihedral : 4.545 21.017 2195 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.02 % Allowed : 21.57 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1710 helix: 0.20 (0.23), residues: 590 sheet: 0.28 (0.29), residues: 345 loop : -0.80 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 259 HIS 0.001 0.000 HIS C 125 PHE 0.032 0.001 PHE D 322 TYR 0.010 0.001 TYR A 91 ARG 0.005 0.000 ARG E 398 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5987.14 seconds wall clock time: 106 minutes 0.69 seconds (6360.69 seconds total)