Starting phenix.real_space_refine on Thu Jun 12 07:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bp0_44756/06_2025/9bp0_44756.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bp0_44756/06_2025/9bp0_44756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bp0_44756/06_2025/9bp0_44756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bp0_44756/06_2025/9bp0_44756.map" model { file = "/net/cci-nas-00/data/ceres_data/9bp0_44756/06_2025/9bp0_44756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bp0_44756/06_2025/9bp0_44756.cif" } resolution = 3.67 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= 0.009 sd= 0.095 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 95 5.16 5 C 8971 2.51 5 N 2200 2.21 5 O 2477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13743 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2750 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 342, 2741 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 342, 2741 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 2801 Chain: "B" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2743 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2728 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2768 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2664 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 192 " occ=0.42 ... (16 atoms not shown) pdb=" OE2BGLU A 192 " occ=0.58 Time building chain proxies: 9.29, per 1000 atoms: 0.68 Number of scatterers: 13743 At special positions: 0 Unit cell: (92.96, 96.28, 137.78, 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 95 16.00 O 2477 8.00 N 2200 7.00 C 8971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 38 " " NAG B 501 " - " ASN B 38 " " NAG C 501 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 23 sheets defined 40.5% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 20 through 23 removed outlier: 3.823A pdb=" N GLY A 23 " --> pdb=" O ARG A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.722A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.312A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 244 removed outlier: 4.568A pdb=" N ILE A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.567A pdb=" N ILE A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 273 Processing helix chain 'A' and resid 281 through 309 Processing helix chain 'A' and resid 388 through 420 Proline residue: A 404 - end of helix Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 20 through 23 removed outlier: 3.928A pdb=" N GLY B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.750A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.925A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 244 removed outlier: 4.523A pdb=" N ILE B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 3.599A pdb=" N ILE B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 273 Processing helix chain 'B' and resid 281 through 309 Processing helix chain 'B' and resid 387 through 420 removed outlier: 4.029A pdb=" N ARG B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.630A pdb=" N GLY C 23 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.751A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.737A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 242 removed outlier: 5.158A pdb=" N ILE C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 248 through 273 removed outlier: 3.752A pdb=" N THR C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.685A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 420 Proline residue: C 404 - end of helix Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.789A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 243 removed outlier: 4.465A pdb=" N ILE D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 271 removed outlier: 3.842A pdb=" N ARG D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 Processing helix chain 'D' and resid 388 through 420 Proline residue: D 404 - end of helix Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 92 through 95 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 251 through 268 Processing helix chain 'E' and resid 272 through 297 removed outlier: 3.730A pdb=" N ARG E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Proline residue: E 278 - end of helix removed outlier: 4.018A pdb=" N GLU E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 333 removed outlier: 3.686A pdb=" N VAL E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 475 Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.325A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 105 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.325A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 64 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 132 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 62 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100 removed outlier: 4.574A pdb=" N HIS A 215 " --> pdb=" O AGLU A 192 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N AGLU A 192 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 217 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 190 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.742A pdb=" N GLY A 205 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.805A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.635A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.587A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.452A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.452A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 177 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 100 removed outlier: 4.763A pdb=" N HIS C 215 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU C 192 " --> pdb=" O HIS C 215 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLU C 217 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS C 190 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 201 through 202 Processing sheet with id=AB6, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.769A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 117 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER D 129 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG D 119 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 127 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE D 44 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 106 through 107 removed outlier: 6.041A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE D 44 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.681A pdb=" N GLU D 217 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AC1, first strand: chain 'D' and resid 201 through 202 removed outlier: 3.586A pdb=" N GLY D 205 " --> pdb=" O TYR D 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 107 removed outlier: 4.543A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.941A pdb=" N SER E 128 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AC5, first strand: chain 'E' and resid 172 through 177 removed outlier: 3.818A pdb=" N GLY E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR E 239 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP E 215 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 11.958A pdb=" N ARG E 241 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N LYS E 213 " --> pdb=" O ARG E 241 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2265 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: 4.02 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4227 1.34 - 1.46: 3442 1.46 - 1.58: 6269 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 14092 Sorted by residual: bond pdb=" N ILE E 139 " pdb=" CA ILE E 139 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ASP D 141 " pdb=" CA ASP D 141 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.89e+00 bond pdb=" N LEU E 140 " pdb=" CA LEU E 140 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.79e+00 bond pdb=" N ILE D 389 " pdb=" CA ILE D 389 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.82e+00 bond pdb=" N MET D 140 " pdb=" CA MET D 140 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.17e-02 7.31e+03 6.56e+00 ... (remaining 14087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18851 2.03 - 4.07: 252 4.07 - 6.10: 49 6.10 - 8.13: 5 8.13 - 10.16: 6 Bond angle restraints: 19163 Sorted by residual: angle pdb=" CA ASP D 141 " pdb=" C ASP D 141 " pdb=" O ASP D 141 " ideal model delta sigma weight residual 121.56 117.82 3.74 1.09e+00 8.42e-01 1.17e+01 angle pdb=" CB MET B 89 " pdb=" CG MET B 89 " pdb=" SD MET B 89 " ideal model delta sigma weight residual 112.70 122.14 -9.44 3.00e+00 1.11e-01 9.91e+00 angle pdb=" CA ILE E 139 " pdb=" C ILE E 139 " pdb=" O ILE E 139 " ideal model delta sigma weight residual 120.76 117.36 3.40 1.10e+00 8.26e-01 9.56e+00 angle pdb=" C ALA E 272 " pdb=" N SER E 273 " pdb=" CA SER E 273 " ideal model delta sigma weight residual 120.44 124.34 -3.90 1.30e+00 5.92e-01 8.98e+00 angle pdb=" C ILE E 56 " pdb=" CA ILE E 56 " pdb=" CB ILE E 56 " ideal model delta sigma weight residual 111.00 113.87 -2.87 9.80e-01 1.04e+00 8.55e+00 ... (remaining 19158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7437 17.82 - 35.63: 752 35.63 - 53.45: 221 53.45 - 71.27: 28 71.27 - 89.09: 5 Dihedral angle restraints: 8443 sinusoidal: 3384 harmonic: 5059 Sorted by residual: dihedral pdb=" CB CYS E 221 " pdb=" SG CYS E 221 " pdb=" SG CYS E 233 " pdb=" CB CYS E 233 " ideal model delta sinusoidal sigma weight residual -86.00 -167.55 81.55 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 48.54 44.46 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS B 138 " pdb=" SG CYS B 138 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 50.66 42.34 1 1.00e+01 1.00e-02 2.50e+01 ... (remaining 8440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1804 0.056 - 0.113: 341 0.113 - 0.169: 34 0.169 - 0.225: 4 0.225 - 0.282: 2 Chirality restraints: 2185 Sorted by residual: chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL B 416 " pdb=" CA VAL B 416 " pdb=" CG1 VAL B 416 " pdb=" CG2 VAL B 416 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE D 389 " pdb=" N ILE D 389 " pdb=" C ILE D 389 " pdb=" CB ILE D 389 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2182 not shown) Planarity restraints: 2402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 325 " 0.019 2.00e-02 2.50e+03 1.23e-02 3.04e+00 pdb=" CG TYR E 325 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 325 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 325 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 325 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 325 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 325 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 325 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 239 " 0.014 2.00e-02 2.50e+03 1.10e-02 3.01e+00 pdb=" CG TRP A 239 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 239 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 239 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 239 " 0.014 2.00e-02 2.50e+03 1.06e-02 2.81e+00 pdb=" CG TRP B 239 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 239 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 239 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 239 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 239 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 239 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 239 " 0.003 2.00e-02 2.50e+03 ... (remaining 2399 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 264 2.68 - 3.24: 13394 3.24 - 3.79: 21518 3.79 - 4.35: 26819 4.35 - 4.90: 45207 Nonbonded interactions: 107202 Sorted by model distance: nonbonded pdb=" O LEU D 98 " pdb=" OG1 THR E 135 " model vdw 2.126 3.040 nonbonded pdb=" N ARG D 119 " pdb=" OXT GLY D 502 " model vdw 2.203 3.120 nonbonded pdb=" O ILE A 28 " pdb=" NH2 ARG A 72 " model vdw 2.226 3.120 nonbonded pdb=" O GLY C 19 " pdb=" OG SER C 22 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP C 25 " pdb=" OG SER D 11 " model vdw 2.256 3.040 ... (remaining 107197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 191 or resid 193 through 395 or (resid 396 throu \ gh 401 and (name N or name CA or name C or name O or name CB )) or resid 402 thr \ ough 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) \ or resid 501)) selection = (chain 'B' and (resid 8 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 310 or res \ id 386 through 387 or (resid 388 and (name N or name CA or name C or name O or n \ ame CB )) or resid 389 through 392 or (resid 393 and (name N or name CA or name \ C or name O or name CB )) or resid 394 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 501)) selection = (chain 'C' and (resid 8 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 191 or resid 193 through 387 or (re \ sid 388 and (name N or name CA or name C or name O or name CB )) or resid 389 th \ rough 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) \ or resid 394 through 396 or (resid 397 through 401 and (name N or name CA or na \ me C or name O or name CB )) or resid 402 through 422 or resid 501)) selection = (chain 'D' and (resid 8 through 191 or resid 193 through 310 or resid 386 throug \ h 387 or (resid 388 and (name N or name CA or name C or name O or name CB )) or \ resid 389 through 392 or (resid 393 and (name N or name CA or name C or name O o \ r name CB )) or resid 394 through 396 or (resid 397 through 401 and (name N or n \ ame CA or name C or name O or name CB )) or resid 402 through 421 or (resid 422 \ and (name N or name CA or name C or name O or name CB )) or resid 501)) } 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.780 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14107 Z= 0.162 Angle : 0.620 10.163 19198 Z= 0.315 Chirality : 0.044 0.282 2185 Planarity : 0.003 0.032 2397 Dihedral : 15.348 89.087 5125 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 4.96 % Allowed : 21.65 % Favored : 73.39 % 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: 0.48 (0.21), residues: 1687 helix: 2.39 (0.21), residues: 605 sheet: -0.26 (0.29), residues: 339 loop : -1.19 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 239 HIS 0.003 0.001 HIS C 201 PHE 0.013 0.001 PHE C 407 TYR 0.029 0.001 TYR E 325 ARG 0.003 0.000 ARG C 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 5) link_NAG-ASN : angle 4.06896 ( 15) hydrogen bonds : bond 0.17280 ( 708) hydrogen bonds : angle 7.47829 ( 2265) SS BOND : bond 0.00232 ( 10) SS BOND : angle 1.00170 ( 20) covalent geometry : bond 0.00334 (14092) covalent geometry : angle 0.60917 (19163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 383 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6892 (tt) REVERT: B 35 PRO cc_start: 0.7099 (Cg_endo) cc_final: 0.6625 (Cg_exo) REVERT: B 156 LEU cc_start: 0.6893 (mp) cc_final: 0.6577 (mp) REVERT: B 299 LEU cc_start: 0.8804 (tt) cc_final: 0.8550 (tp) REVERT: C 18 MET cc_start: 0.8651 (mpp) cc_final: 0.8383 (mpp) REVERT: C 246 MET cc_start: 0.5382 (tmm) cc_final: 0.5099 (ttt) REVERT: D 127 LEU cc_start: 0.6545 (tt) cc_final: 0.6120 (tt) REVERT: D 283 ILE cc_start: 0.5989 (OUTLIER) cc_final: 0.5581 (mm) REVERT: E 256 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8425 (mm) REVERT: E 322 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7034 (tm) outliers start: 74 outliers final: 30 residues processed: 432 average time/residue: 0.2136 time to fit residues: 140.5027 Evaluate side-chains 315 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN B 109 HIS ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN C 150 GLN C 155 GLN D 102 ASN D 150 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.165247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139523 restraints weight = 30576.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139289 restraints weight = 26546.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141522 restraints weight = 21075.602| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14107 Z= 0.169 Angle : 0.717 12.361 19198 Z= 0.360 Chirality : 0.047 0.283 2185 Planarity : 0.004 0.045 2397 Dihedral : 7.289 75.373 2002 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.97 % Allowed : 22.92 % Favored : 71.11 % 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: 0.60 (0.21), residues: 1687 helix: 2.36 (0.21), residues: 598 sheet: -0.02 (0.29), residues: 352 loop : -1.07 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 286 HIS 0.006 0.001 HIS A 109 PHE 0.030 0.002 PHE B 410 TYR 0.027 0.002 TYR E 325 ARG 0.007 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 5) link_NAG-ASN : angle 4.16662 ( 15) hydrogen bonds : bond 0.04135 ( 708) hydrogen bonds : angle 5.25835 ( 2265) SS BOND : bond 0.00649 ( 10) SS BOND : angle 3.24476 ( 20) covalent geometry : bond 0.00363 (14092) covalent geometry : angle 0.70031 (19163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 297 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7069 (tt) REVERT: B 299 LEU cc_start: 0.8820 (tt) cc_final: 0.8553 (tp) REVERT: C 18 MET cc_start: 0.8560 (mpp) cc_final: 0.8331 (mpp) REVERT: C 246 MET cc_start: 0.5409 (tmm) cc_final: 0.4990 (ttt) REVERT: C 293 PHE cc_start: 0.7611 (m-10) cc_final: 0.7307 (m-10) REVERT: D 263 MET cc_start: 0.5893 (mmm) cc_final: 0.5620 (mmm) REVERT: E 114 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7678 (ttmt) REVERT: E 322 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6960 (tm) outliers start: 89 outliers final: 46 residues processed: 354 average time/residue: 0.2188 time to fit residues: 118.2511 Evaluate side-chains 304 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 2 optimal weight: 0.0170 chunk 56 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 140 optimal weight: 0.0970 chunk 152 optimal weight: 3.9990 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN C 155 GLN D 219 GLN E 178 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124836 restraints weight = 37451.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127302 restraints weight = 26866.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128163 restraints weight = 19627.240| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14107 Z= 0.143 Angle : 0.688 10.794 19198 Z= 0.340 Chirality : 0.046 0.275 2185 Planarity : 0.004 0.073 2397 Dihedral : 6.900 76.237 1984 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.76 % Allowed : 22.72 % Favored : 71.51 % 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: 0.69 (0.21), residues: 1687 helix: 2.37 (0.21), residues: 595 sheet: 0.15 (0.29), residues: 347 loop : -1.01 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 239 HIS 0.005 0.001 HIS B 215 PHE 0.026 0.002 PHE B 295 TYR 0.022 0.001 TYR E 325 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 5) link_NAG-ASN : angle 3.83366 ( 15) hydrogen bonds : bond 0.03721 ( 708) hydrogen bonds : angle 4.77068 ( 2265) SS BOND : bond 0.00448 ( 10) SS BOND : angle 2.47734 ( 20) covalent geometry : bond 0.00318 (14092) covalent geometry : angle 0.67587 (19163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 267 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 THR cc_start: 0.6782 (OUTLIER) cc_final: 0.6233 (p) REVERT: A 232 LEU cc_start: 0.8741 (tp) cc_final: 0.8477 (tt) REVERT: A 246 MET cc_start: 0.7546 (ppp) cc_final: 0.6710 (ppp) REVERT: B 197 TYR cc_start: 0.7666 (m-10) cc_final: 0.7460 (m-10) REVERT: B 299 LEU cc_start: 0.8874 (tt) cc_final: 0.8535 (tp) REVERT: C 138 CYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6643 (p) REVERT: C 246 MET cc_start: 0.5310 (tmm) cc_final: 0.4791 (ttt) REVERT: C 293 PHE cc_start: 0.7553 (m-10) cc_final: 0.7266 (m-10) REVERT: D 129 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7245 (p) REVERT: D 195 LEU cc_start: 0.7689 (mt) cc_final: 0.7436 (mp) REVERT: E 77 MET cc_start: 0.7547 (mpp) cc_final: 0.7147 (mtt) REVERT: E 113 TYR cc_start: 0.7647 (t80) cc_final: 0.7399 (t80) REVERT: E 133 ASP cc_start: 0.6440 (p0) cc_final: 0.6166 (p0) REVERT: E 322 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7120 (tm) outliers start: 86 outliers final: 52 residues processed: 325 average time/residue: 0.2173 time to fit residues: 108.0546 Evaluate side-chains 290 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN C 266 GLN D 155 GLN E 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124951 restraints weight = 32883.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124244 restraints weight = 25375.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125943 restraints weight = 21582.002| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14107 Z= 0.146 Angle : 0.673 10.742 19198 Z= 0.333 Chirality : 0.045 0.291 2185 Planarity : 0.004 0.032 2397 Dihedral : 6.849 73.366 1978 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.23 % Allowed : 24.06 % Favored : 70.71 % 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: 0.71 (0.21), residues: 1687 helix: 2.37 (0.21), residues: 596 sheet: 0.03 (0.28), residues: 356 loop : -0.90 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 239 HIS 0.006 0.001 HIS C 201 PHE 0.041 0.002 PHE E 282 TYR 0.018 0.002 TYR C 222 ARG 0.009 0.001 ARG D 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 5) link_NAG-ASN : angle 3.98377 ( 15) hydrogen bonds : bond 0.03292 ( 708) hydrogen bonds : angle 4.57482 ( 2265) SS BOND : bond 0.00618 ( 10) SS BOND : angle 2.77406 ( 20) covalent geometry : bond 0.00331 (14092) covalent geometry : angle 0.65867 (19163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 244 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7735 (tt0) REVERT: A 116 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7643 (mtpt) REVERT: A 232 LEU cc_start: 0.8813 (tp) cc_final: 0.8594 (tt) REVERT: A 246 MET cc_start: 0.7419 (ppp) cc_final: 0.6743 (ppp) REVERT: B 299 LEU cc_start: 0.8855 (tt) cc_final: 0.8506 (tp) REVERT: B 300 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7443 (tm-30) REVERT: C 246 MET cc_start: 0.5332 (tmm) cc_final: 0.5063 (ttt) REVERT: C 293 PHE cc_start: 0.7658 (m-10) cc_final: 0.7254 (m-10) REVERT: D 129 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7855 (p) REVERT: E 77 MET cc_start: 0.7713 (mpp) cc_final: 0.7398 (mtt) REVERT: E 113 TYR cc_start: 0.7759 (t80) cc_final: 0.7467 (t80) REVERT: E 133 ASP cc_start: 0.6859 (p0) cc_final: 0.6495 (p0) REVERT: E 217 GLU cc_start: 0.7592 (tt0) cc_final: 0.7357 (tt0) REVERT: E 322 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7129 (tm) outliers start: 78 outliers final: 58 residues processed: 298 average time/residue: 0.2087 time to fit residues: 98.2715 Evaluate side-chains 283 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.151375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124005 restraints weight = 42087.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126037 restraints weight = 32828.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127267 restraints weight = 21827.543| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14107 Z= 0.141 Angle : 0.675 10.317 19198 Z= 0.332 Chirality : 0.046 0.385 2185 Planarity : 0.003 0.029 2397 Dihedral : 6.720 59.711 1978 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.29 % Allowed : 24.06 % Favored : 70.64 % 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: 0.87 (0.21), residues: 1687 helix: 2.52 (0.21), residues: 590 sheet: 0.11 (0.29), residues: 356 loop : -0.80 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 239 HIS 0.006 0.001 HIS B 215 PHE 0.021 0.001 PHE E 282 TYR 0.017 0.001 TYR E 470 ARG 0.004 0.000 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 5) link_NAG-ASN : angle 4.57865 ( 15) hydrogen bonds : bond 0.03254 ( 708) hydrogen bonds : angle 4.49355 ( 2265) SS BOND : bond 0.00579 ( 10) SS BOND : angle 3.31846 ( 20) covalent geometry : bond 0.00320 (14092) covalent geometry : angle 0.65473 (19163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 220 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 299 LEU cc_start: 0.8850 (tt) cc_final: 0.8535 (tp) REVERT: C 246 MET cc_start: 0.5295 (tmm) cc_final: 0.4875 (ttt) REVERT: C 293 PHE cc_start: 0.7606 (m-10) cc_final: 0.7230 (m-10) REVERT: D 283 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7175 (mm) REVERT: E 133 ASP cc_start: 0.7215 (p0) cc_final: 0.6813 (p0) REVERT: E 322 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7321 (tm) REVERT: E 474 TYR cc_start: 0.5580 (m-10) cc_final: 0.5253 (m-80) outliers start: 79 outliers final: 58 residues processed: 279 average time/residue: 0.2109 time to fit residues: 94.3888 Evaluate side-chains 265 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 125 ASN E 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122822 restraints weight = 37186.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124726 restraints weight = 24856.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125256 restraints weight = 22085.216| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14107 Z= 0.148 Angle : 0.721 25.187 19198 Z= 0.343 Chirality : 0.062 1.944 2185 Planarity : 0.003 0.030 2397 Dihedral : 6.891 59.200 1978 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.56 % Allowed : 23.99 % Favored : 70.44 % 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: 0.87 (0.21), residues: 1687 helix: 2.52 (0.21), residues: 593 sheet: 0.12 (0.29), residues: 349 loop : -0.81 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 239 HIS 0.003 0.001 HIS D 201 PHE 0.035 0.001 PHE B 410 TYR 0.016 0.001 TYR E 325 ARG 0.009 0.000 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01403 ( 5) link_NAG-ASN : angle 8.69422 ( 15) hydrogen bonds : bond 0.03087 ( 708) hydrogen bonds : angle 4.45741 ( 2265) SS BOND : bond 0.00950 ( 10) SS BOND : angle 3.04546 ( 20) covalent geometry : bond 0.00329 (14092) covalent geometry : angle 0.67279 (19163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7580 (mmm) REVERT: A 116 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7957 (mtpt) REVERT: A 293 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.7112 (t80) REVERT: B 299 LEU cc_start: 0.8790 (tt) cc_final: 0.8555 (tp) REVERT: C 246 MET cc_start: 0.5310 (tmm) cc_final: 0.4901 (ttt) REVERT: D 283 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7350 (mm) REVERT: E 77 MET cc_start: 0.7702 (mtt) cc_final: 0.7460 (mtt) REVERT: E 133 ASP cc_start: 0.7259 (p0) cc_final: 0.6874 (p0) REVERT: E 282 PHE cc_start: 0.7592 (t80) cc_final: 0.7301 (t80) REVERT: E 322 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7496 (tm) REVERT: E 474 TYR cc_start: 0.6015 (m-10) cc_final: 0.5680 (m-80) outliers start: 83 outliers final: 65 residues processed: 276 average time/residue: 0.1989 time to fit residues: 86.9928 Evaluate side-chains 266 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 55 optimal weight: 0.0370 chunk 99 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120751 restraints weight = 50981.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125160 restraints weight = 54767.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128702 restraints weight = 17273.503| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14107 Z= 0.174 Angle : 0.754 20.107 19198 Z= 0.363 Chirality : 0.048 0.543 2185 Planarity : 0.004 0.072 2397 Dihedral : 6.858 59.150 1978 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.43 % Allowed : 24.53 % Favored : 70.04 % 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: 0.69 (0.21), residues: 1687 helix: 2.39 (0.21), residues: 592 sheet: 0.02 (0.28), residues: 353 loop : -0.94 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 239 HIS 0.007 0.001 HIS B 215 PHE 0.028 0.002 PHE E 182 TYR 0.019 0.002 TYR A 58 ARG 0.018 0.001 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.01127 ( 5) link_NAG-ASN : angle 8.46700 ( 15) hydrogen bonds : bond 0.03383 ( 708) hydrogen bonds : angle 4.47781 ( 2265) SS BOND : bond 0.00483 ( 10) SS BOND : angle 2.99498 ( 20) covalent geometry : bond 0.00401 (14092) covalent geometry : angle 0.71039 (19163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 229 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8146 (mtmt) REVERT: A 412 ILE cc_start: 0.7184 (tp) cc_final: 0.6634 (mm) REVERT: C 246 MET cc_start: 0.5400 (tmm) cc_final: 0.4978 (ttm) REVERT: D 43 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8946 (mt) REVERT: E 113 TYR cc_start: 0.8160 (t80) cc_final: 0.7846 (t80) REVERT: E 130 ASN cc_start: 0.8204 (t0) cc_final: 0.7932 (t0) REVERT: E 187 ASP cc_start: 0.7599 (m-30) cc_final: 0.7295 (t0) REVERT: E 322 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7625 (tm) outliers start: 81 outliers final: 62 residues processed: 282 average time/residue: 0.2041 time to fit residues: 90.3332 Evaluate side-chains 277 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 212 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110301 restraints weight = 44340.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116405 restraints weight = 16653.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120394 restraints weight = 7758.807| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14107 Z= 0.143 Angle : 0.716 20.655 19198 Z= 0.345 Chirality : 0.047 0.555 2185 Planarity : 0.004 0.033 2397 Dihedral : 6.762 59.954 1977 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.69 % Allowed : 24.46 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1687 helix: 2.37 (0.21), residues: 598 sheet: 0.09 (0.29), residues: 350 loop : -0.95 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 239 HIS 0.003 0.001 HIS D 201 PHE 0.032 0.001 PHE B 410 TYR 0.015 0.001 TYR E 325 ARG 0.006 0.000 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01345 ( 5) link_NAG-ASN : angle 8.04772 ( 15) hydrogen bonds : bond 0.03210 ( 708) hydrogen bonds : angle 4.46930 ( 2265) SS BOND : bond 0.00493 ( 10) SS BOND : angle 2.77472 ( 20) covalent geometry : bond 0.00328 (14092) covalent geometry : angle 0.67468 (19163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6675 (t80) REVERT: A 412 ILE cc_start: 0.7150 (tp) cc_final: 0.6788 (mm) REVERT: C 103 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: C 227 MET cc_start: 0.8268 (ppp) cc_final: 0.7418 (ppp) REVERT: C 246 MET cc_start: 0.5242 (tmm) cc_final: 0.4602 (ttm) REVERT: C 293 PHE cc_start: 0.7236 (m-10) cc_final: 0.7025 (m-10) REVERT: D 43 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8931 (mt) REVERT: D 147 MET cc_start: 0.7265 (mtt) cc_final: 0.7015 (mtp) REVERT: D 415 TRP cc_start: 0.7811 (m100) cc_final: 0.7600 (m100) REVERT: E 113 TYR cc_start: 0.8208 (t80) cc_final: 0.7963 (t80) REVERT: E 130 ASN cc_start: 0.8306 (t0) cc_final: 0.7917 (t0) REVERT: E 187 ASP cc_start: 0.8308 (m-30) cc_final: 0.7432 (t0) REVERT: E 322 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7747 (tm) outliers start: 70 outliers final: 57 residues processed: 275 average time/residue: 0.2085 time to fit residues: 90.4890 Evaluate side-chains 277 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 45 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 0.0050 chunk 158 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 53 optimal weight: 0.0670 chunk 68 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 overall best weight: 1.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110479 restraints weight = 36603.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115513 restraints weight = 15129.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118819 restraints weight = 8568.997| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14107 Z= 0.141 Angle : 0.726 19.313 19198 Z= 0.348 Chirality : 0.046 0.341 2185 Planarity : 0.004 0.032 2397 Dihedral : 6.886 59.173 1975 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.49 % Allowed : 24.87 % Favored : 70.64 % 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 (0.21), residues: 1687 helix: 2.32 (0.21), residues: 594 sheet: 0.07 (0.28), residues: 355 loop : -1.02 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 239 HIS 0.005 0.001 HIS D 201 PHE 0.020 0.001 PHE B 410 TYR 0.016 0.001 TYR E 325 ARG 0.010 0.000 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01209 ( 5) link_NAG-ASN : angle 7.64214 ( 15) hydrogen bonds : bond 0.03195 ( 708) hydrogen bonds : angle 4.47121 ( 2265) SS BOND : bond 0.00495 ( 10) SS BOND : angle 2.81095 ( 20) covalent geometry : bond 0.00325 (14092) covalent geometry : angle 0.68869 (19163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8578 (t80) REVERT: A 276 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7968 (mmtm) REVERT: A 412 ILE cc_start: 0.7257 (tp) cc_final: 0.6906 (mm) REVERT: B 57 ASP cc_start: 0.7779 (p0) cc_final: 0.7484 (p0) REVERT: B 293 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6855 (t80) REVERT: B 300 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6747 (mm-30) REVERT: C 33 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8233 (mmmt) REVERT: C 103 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: C 227 MET cc_start: 0.8250 (ppp) cc_final: 0.7429 (ppp) REVERT: C 246 MET cc_start: 0.5039 (tmm) cc_final: 0.4336 (ttm) REVERT: C 293 PHE cc_start: 0.7157 (m-10) cc_final: 0.6943 (m-10) REVERT: D 43 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8976 (mt) REVERT: D 163 MET cc_start: 0.8175 (ttp) cc_final: 0.7933 (ttp) REVERT: D 415 TRP cc_start: 0.7949 (m100) cc_final: 0.7738 (m100) REVERT: E 130 ASN cc_start: 0.8282 (t0) cc_final: 0.7904 (t0) REVERT: E 187 ASP cc_start: 0.8420 (m-30) cc_final: 0.7533 (t0) REVERT: E 322 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7785 (tm) outliers start: 67 outliers final: 49 residues processed: 258 average time/residue: 0.2053 time to fit residues: 82.8226 Evaluate side-chains 263 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 144 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 64 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 0.0050 chunk 126 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111387 restraints weight = 47202.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118662 restraints weight = 18065.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120928 restraints weight = 8686.171| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14107 Z= 0.122 Angle : 0.702 17.957 19198 Z= 0.335 Chirality : 0.045 0.279 2185 Planarity : 0.003 0.033 2397 Dihedral : 6.797 59.668 1974 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.35 % Allowed : 25.60 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1687 helix: 2.44 (0.21), residues: 593 sheet: 0.21 (0.28), residues: 353 loop : -0.90 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 239 HIS 0.003 0.001 HIS D 201 PHE 0.020 0.001 PHE E 282 TYR 0.022 0.001 TYR E 113 ARG 0.009 0.000 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01255 ( 5) link_NAG-ASN : angle 7.12208 ( 15) hydrogen bonds : bond 0.03013 ( 708) hydrogen bonds : angle 4.43968 ( 2265) SS BOND : bond 0.00498 ( 10) SS BOND : angle 2.86018 ( 20) covalent geometry : bond 0.00269 (14092) covalent geometry : angle 0.66707 (19163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8558 (t80) REVERT: A 412 ILE cc_start: 0.7239 (tp) cc_final: 0.6901 (mm) REVERT: B 293 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6799 (t80) REVERT: C 33 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8140 (mmmt) REVERT: C 56 MET cc_start: 0.7989 (mtt) cc_final: 0.7745 (mtt) REVERT: C 103 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: C 188 LEU cc_start: 0.8358 (mt) cc_final: 0.7813 (tp) REVERT: C 227 MET cc_start: 0.8153 (ppp) cc_final: 0.7380 (ppp) REVERT: C 246 MET cc_start: 0.4937 (tmm) cc_final: 0.4164 (ttm) REVERT: D 111 VAL cc_start: 0.8335 (t) cc_final: 0.7988 (m) REVERT: E 109 ASP cc_start: 0.5355 (OUTLIER) cc_final: 0.5096 (m-30) REVERT: E 130 ASN cc_start: 0.8130 (t0) cc_final: 0.7870 (t0) REVERT: E 187 ASP cc_start: 0.8349 (m-30) cc_final: 0.7539 (t0) REVERT: E 322 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7663 (tm) outliers start: 50 outliers final: 39 residues processed: 253 average time/residue: 0.2068 time to fit residues: 82.3090 Evaluate side-chains 245 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 TRP Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100643 restraints weight = 39117.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105444 restraints weight = 16204.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108621 restraints weight = 9238.159| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.8229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 14107 Z= 0.333 Angle : 0.874 17.843 19198 Z= 0.431 Chirality : 0.052 0.408 2185 Planarity : 0.005 0.051 2397 Dihedral : 7.118 58.021 1972 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.82 % Allowed : 25.60 % Favored : 70.58 % 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: 0.14 (0.20), residues: 1687 helix: 1.83 (0.21), residues: 606 sheet: -0.29 (0.27), residues: 359 loop : -1.21 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 239 HIS 0.006 0.002 HIS C 201 PHE 0.035 0.003 PHE C 44 TYR 0.021 0.002 TYR D 128 ARG 0.010 0.001 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 5) link_NAG-ASN : angle 7.92191 ( 15) hydrogen bonds : bond 0.04032 ( 708) hydrogen bonds : angle 4.78688 ( 2265) SS BOND : bond 0.00583 ( 10) SS BOND : angle 3.57859 ( 20) covalent geometry : bond 0.00795 (14092) covalent geometry : angle 0.83800 (19163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.31 seconds wall clock time: 82 minutes 20.89 seconds (4940.89 seconds total)