Starting phenix.real_space_refine on Thu Sep 18 03:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bp0_44756/09_2025/9bp0_44756.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bp0_44756/09_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_44756/09_2025/9bp0_44756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bp0_44756/09_2025/9bp0_44756.map" model { file = "/net/cci-nas-00/data/ceres_data/9bp0_44756/09_2025/9bp0_44756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bp0_44756/09_2025/9bp0_44756.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 1, '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: {'ARG:plan': 4, 'GLU:plan': 1, '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: {'ARG:plan': 3, 'GLU:plan': 2, '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: {'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} 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: 3.72, per 1000 atoms: 0.27 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: 1.01 Conformation dependent library (CDL) restraints added in 713.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.42 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: 2.34 Time building geometry restraints manager: 1.39 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 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: 1.790 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 271 TYR 0.029 0.001 TYR E 325 PHE 0.013 0.001 PHE C 407 TRP 0.029 0.001 TRP A 239 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00334 (14092) covalent geometry : angle 0.60917 (19163) SS BOND : bond 0.00232 ( 10) SS BOND : angle 1.00170 ( 20) hydrogen bonds : bond 0.17280 ( 708) hydrogen bonds : angle 7.47829 ( 2265) link_NAG-ASN : bond 0.00592 ( 5) link_NAG-ASN : angle 4.06896 ( 15) *********************** 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 : 0.493 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: 0.1003 time to fit residues: 66.8237 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 : 0.476 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.165271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139679 restraints weight = 31562.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138489 restraints weight = 28167.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141267 restraints weight = 21942.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141780 restraints weight = 12783.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142674 restraints weight = 12368.756| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2323 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= 0.160 Angle : 0.711 10.980 19198 Z= 0.357 Chirality : 0.047 0.283 2185 Planarity : 0.004 0.044 2397 Dihedral : 7.266 75.759 2002 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 6.17 % Allowed : 22.92 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.21), residues: 1687 helix: 2.37 (0.21), residues: 598 sheet: 0.02 (0.29), residues: 351 loop : -1.06 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 72 TYR 0.027 0.002 TYR D 301 PHE 0.029 0.002 PHE B 410 TRP 0.022 0.002 TRP B 286 HIS 0.006 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00348 (14092) covalent geometry : angle 0.69473 (19163) SS BOND : bond 0.00659 ( 10) SS BOND : angle 3.23341 ( 20) hydrogen bonds : bond 0.03965 ( 708) hydrogen bonds : angle 5.26777 ( 2265) link_NAG-ASN : bond 0.00625 ( 5) link_NAG-ASN : angle 4.11156 ( 15) *********************** 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 391 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 299 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6998 (tt) REVERT: A 210 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7716 (mt) REVERT: A 232 LEU cc_start: 0.8610 (tp) cc_final: 0.8392 (tt) REVERT: B 299 LEU cc_start: 0.8826 (tt) cc_final: 0.8556 (tp) REVERT: C 246 MET cc_start: 0.5446 (tmm) cc_final: 0.4962 (ttt) REVERT: C 293 PHE cc_start: 0.7584 (m-10) cc_final: 0.7280 (m-10) REVERT: D 263 MET cc_start: 0.5945 (mmm) cc_final: 0.5653 (mmm) REVERT: E 114 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7663 (ttmt) REVERT: E 133 ASP cc_start: 0.6074 (p0) cc_final: 0.5873 (p0) REVERT: E 322 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6993 (tm) outliers start: 92 outliers final: 46 residues processed: 359 average time/residue: 0.1036 time to fit residues: 57.4679 Evaluate side-chains 309 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 210 ILE 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 90 LEU 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 176 VAL Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 216 LEU 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 162 THR 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 110 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 0.0770 chunk 144 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126534 restraints weight = 40087.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128789 restraints weight = 36335.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130929 restraints weight = 22377.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132063 restraints weight = 13352.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134506 restraints weight = 11386.964| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3267 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= 0.135 Angle : 0.681 11.148 19198 Z= 0.335 Chirality : 0.045 0.269 2185 Planarity : 0.004 0.028 2397 Dihedral : 6.877 76.458 1984 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.83 % Allowed : 22.99 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.21), residues: 1687 helix: 2.35 (0.21), residues: 595 sheet: 0.22 (0.29), residues: 344 loop : -1.03 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 27 TYR 0.022 0.001 TYR E 325 PHE 0.021 0.002 PHE B 293 TRP 0.019 0.001 TRP A 239 HIS 0.005 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00295 (14092) covalent geometry : angle 0.66832 (19163) SS BOND : bond 0.00509 ( 10) SS BOND : angle 2.64553 ( 20) hydrogen bonds : bond 0.03678 ( 708) hydrogen bonds : angle 4.79678 ( 2265) link_NAG-ASN : bond 0.00554 ( 5) link_NAG-ASN : angle 3.78231 ( 15) *********************** 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 351 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 264 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 THR cc_start: 0.6317 (OUTLIER) cc_final: 0.5647 (p) REVERT: A 232 LEU cc_start: 0.8687 (tp) cc_final: 0.8395 (tt) REVERT: A 246 MET cc_start: 0.7311 (ppp) cc_final: 0.6540 (ppp) REVERT: B 299 LEU cc_start: 0.8835 (tt) cc_final: 0.8573 (tp) REVERT: C 138 CYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6566 (p) REVERT: C 140 MET cc_start: 0.6114 (mtt) cc_final: 0.5561 (mtt) REVERT: C 246 MET cc_start: 0.5349 (tmm) cc_final: 0.4894 (ttt) REVERT: C 293 PHE cc_start: 0.7640 (m-10) cc_final: 0.7342 (m-10) REVERT: D 129 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.7142 (p) REVERT: E 133 ASP cc_start: 0.6390 (p0) cc_final: 0.6168 (p0) REVERT: E 322 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.7017 (tm) outliers start: 87 outliers final: 51 residues processed: 322 average time/residue: 0.0993 time to fit residues: 49.4236 Evaluate side-chains 298 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 117 LEU Chi-restraints excluded: chain B residue 149 VAL 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 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 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 C residue 236 ILE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 141 ASP 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 149 VAL Chi-restraints excluded: chain E residue 153 MET 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 289 SER 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 1 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 138 optimal weight: 0.0570 chunk 111 optimal weight: 0.0050 chunk 156 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 226 GLN C 266 GLN D 155 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125585 restraints weight = 28469.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126467 restraints weight = 21150.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128405 restraints weight = 15676.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128909 restraints weight = 10788.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129301 restraints weight = 9614.175| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14107 Z= 0.123 Angle : 0.645 11.307 19198 Z= 0.318 Chirality : 0.045 0.270 2185 Planarity : 0.003 0.029 2397 Dihedral : 6.726 75.224 1977 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.96 % Allowed : 23.59 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1687 helix: 2.43 (0.21), residues: 595 sheet: 0.28 (0.29), residues: 345 loop : -0.96 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.018 0.001 TYR E 325 PHE 0.038 0.001 PHE B 410 TRP 0.018 0.001 TRP A 239 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00264 (14092) covalent geometry : angle 0.63094 (19163) SS BOND : bond 0.01013 ( 10) SS BOND : angle 2.74363 ( 20) hydrogen bonds : bond 0.03234 ( 708) hydrogen bonds : angle 4.56454 ( 2265) link_NAG-ASN : bond 0.00593 ( 5) link_NAG-ASN : angle 3.75133 ( 15) *********************** 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 326 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 252 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8746 (tp) cc_final: 0.8465 (tt) REVERT: A 246 MET cc_start: 0.7327 (ppp) cc_final: 0.6664 (ppp) REVERT: B 299 LEU cc_start: 0.8871 (tt) cc_final: 0.8515 (tp) REVERT: C 246 MET cc_start: 0.5272 (tmm) cc_final: 0.4905 (ttt) REVERT: C 293 PHE cc_start: 0.7589 (m-10) cc_final: 0.7239 (m-10) REVERT: D 129 SER cc_start: 0.7737 (OUTLIER) cc_final: 0.7296 (p) REVERT: D 283 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6516 (mm) REVERT: E 77 MET cc_start: 0.7537 (mpp) cc_final: 0.7151 (mtt) REVERT: E 133 ASP cc_start: 0.6492 (p0) cc_final: 0.6080 (p0) REVERT: E 217 GLU cc_start: 0.7350 (tt0) cc_final: 0.7140 (tt0) REVERT: E 322 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7075 (tm) outliers start: 74 outliers final: 52 residues processed: 302 average time/residue: 0.0977 time to fit residues: 47.0386 Evaluate side-chains 294 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN 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 130 ILE 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 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 43 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 285 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 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 285 ILE 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 149 VAL 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 181 SER 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 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 122 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 125 ASN E 178 GLN E 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120938 restraints weight = 40805.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123734 restraints weight = 31018.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123785 restraints weight = 22289.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125363 restraints weight = 12865.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127546 restraints weight = 10474.352| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14107 Z= 0.228 Angle : 0.827 16.773 19198 Z= 0.413 Chirality : 0.050 0.356 2185 Planarity : 0.005 0.089 2397 Dihedral : 7.255 72.703 1976 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 6.10 % Allowed : 23.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.21), residues: 1687 helix: 2.09 (0.21), residues: 598 sheet: -0.13 (0.28), residues: 351 loop : -1.02 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 48 TYR 0.019 0.002 TYR B 414 PHE 0.023 0.002 PHE C 108 TRP 0.047 0.002 TRP B 94 HIS 0.010 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00527 (14092) covalent geometry : angle 0.81136 (19163) SS BOND : bond 0.01372 ( 10) SS BOND : angle 3.01812 ( 20) hydrogen bonds : bond 0.03845 ( 708) hydrogen bonds : angle 4.71068 ( 2265) link_NAG-ASN : bond 0.00577 ( 5) link_NAG-ASN : angle 4.75240 ( 15) *********************** 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 332 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 241 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7929 (tt0) REVERT: A 156 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 299 LEU cc_start: 0.8815 (tt) cc_final: 0.8439 (tp) REVERT: C 246 MET cc_start: 0.5401 (tmm) cc_final: 0.5056 (ttt) REVERT: D 223 TYR cc_start: 0.7890 (m-80) cc_final: 0.7659 (m-80) REVERT: E 76 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8258 (m) REVERT: E 187 ASP cc_start: 0.7538 (m-30) cc_final: 0.7281 (t0) REVERT: E 322 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7753 (tm) outliers start: 91 outliers final: 57 residues processed: 302 average time/residue: 0.1023 time to fit residues: 48.5494 Evaluate side-chains 267 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 149 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE 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 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 198 CYS Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 289 VAL 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 236 ILE Chi-restraints excluded: chain C residue 285 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 156 LEU 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 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 75 THR Chi-restraints excluded: chain E residue 76 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 181 SER 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 312 ILE 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 136 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN E 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120128 restraints weight = 32470.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119477 restraints weight = 23292.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121164 restraints weight = 20834.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122387 restraints weight = 12746.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123051 restraints weight = 11236.933| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14107 Z= 0.178 Angle : 0.722 11.960 19198 Z= 0.356 Chirality : 0.046 0.336 2185 Planarity : 0.004 0.033 2397 Dihedral : 6.785 62.565 1973 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.36 % Allowed : 24.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.21), residues: 1687 helix: 2.26 (0.21), residues: 593 sheet: -0.12 (0.28), residues: 355 loop : -1.08 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 174 TYR 0.017 0.002 TYR C 24 PHE 0.049 0.002 PHE E 182 TRP 0.037 0.002 TRP C 239 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00414 (14092) covalent geometry : angle 0.70277 (19163) SS BOND : bond 0.00780 ( 10) SS BOND : angle 3.39037 ( 20) hydrogen bonds : bond 0.03510 ( 708) hydrogen bonds : angle 4.59347 ( 2265) link_NAG-ASN : bond 0.00661 ( 5) link_NAG-ASN : angle 4.58877 ( 15) *********************** 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 301 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 ILE cc_start: 0.7278 (tp) cc_final: 0.6733 (mm) REVERT: C 246 MET cc_start: 0.5519 (tmm) cc_final: 0.5040 (ttm) REVERT: D 223 TYR cc_start: 0.7859 (m-80) cc_final: 0.7552 (m-80) REVERT: E 77 MET cc_start: 0.7819 (mtt) cc_final: 0.7475 (mtt) REVERT: E 78 ASP cc_start: 0.8361 (p0) cc_final: 0.8041 (p0) REVERT: E 113 TYR cc_start: 0.8141 (t80) cc_final: 0.7912 (t80) REVERT: E 187 ASP cc_start: 0.7616 (m-30) cc_final: 0.7398 (t0) REVERT: E 322 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7733 (tm) outliers start: 80 outliers final: 55 residues processed: 282 average time/residue: 0.0999 time to fit residues: 44.7187 Evaluate side-chains 261 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 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 88 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 LEU 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 192 GLU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 243 TRP 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 111 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 217 GLU 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 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 200 GLN 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 316 LEU 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 109 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108137 restraints weight = 51487.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115248 restraints weight = 18728.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118826 restraints weight = 8213.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119723 restraints weight = 5437.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119753 restraints weight = 4999.822| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14107 Z= 0.144 Angle : 0.705 13.282 19198 Z= 0.345 Chirality : 0.046 0.318 2185 Planarity : 0.004 0.035 2397 Dihedral : 6.531 58.583 1971 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.22 % Allowed : 25.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.21), residues: 1687 helix: 2.32 (0.21), residues: 592 sheet: -0.02 (0.28), residues: 356 loop : -1.06 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 174 TYR 0.016 0.001 TYR E 325 PHE 0.030 0.001 PHE E 182 TRP 0.039 0.002 TRP C 239 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00329 (14092) covalent geometry : angle 0.68912 (19163) SS BOND : bond 0.00553 ( 10) SS BOND : angle 2.87353 ( 20) hydrogen bonds : bond 0.03341 ( 708) hydrogen bonds : angle 4.51303 ( 2265) link_NAG-ASN : bond 0.00601 ( 5) link_NAG-ASN : angle 4.36784 ( 15) *********************** 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 268 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 ILE cc_start: 0.7172 (tp) cc_final: 0.6786 (mm) REVERT: B 57 ASP cc_start: 0.7884 (p0) cc_final: 0.7612 (p0) REVERT: C 227 MET cc_start: 0.8335 (ppp) cc_final: 0.7530 (ppp) REVERT: C 246 MET cc_start: 0.5185 (tmm) cc_final: 0.4535 (ttm) REVERT: D 223 TYR cc_start: 0.7990 (m-80) cc_final: 0.7531 (m-80) REVERT: E 113 TYR cc_start: 0.8232 (t80) cc_final: 0.7959 (t80) REVERT: E 187 ASP cc_start: 0.8309 (m-30) cc_final: 0.7470 (t0) REVERT: E 322 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7788 (tm) outliers start: 63 outliers final: 50 residues processed: 256 average time/residue: 0.0961 time to fit residues: 39.3968 Evaluate side-chains 249 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 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 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 198 CYS 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 43 ILE Chi-restraints excluded: chain C residue 54 THR 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 129 SER Chi-restraints excluded: chain D residue 189 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 167 LEU Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 200 GLN 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 316 LEU 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 120 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 78 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 140 optimal weight: 0.0040 chunk 153 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.4196 ------------------------------------------------------------------------------- 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 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 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 = 0.3770 r_free = 0.3770 target = 0.145184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107735 restraints weight = 39614.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112870 restraints weight = 15930.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116180 restraints weight = 8877.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118301 restraints weight = 6074.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119639 restraints weight = 4776.020| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.7286 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= 0.150 Angle : 0.698 12.198 19198 Z= 0.340 Chirality : 0.046 0.312 2185 Planarity : 0.004 0.036 2397 Dihedral : 6.473 58.293 1971 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.36 % Allowed : 24.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.21), residues: 1687 helix: 2.34 (0.21), residues: 597 sheet: 0.02 (0.28), residues: 355 loop : -1.04 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.016 0.001 TYR E 325 PHE 0.031 0.002 PHE B 410 TRP 0.049 0.002 TRP D 239 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00348 (14092) covalent geometry : angle 0.68185 (19163) SS BOND : bond 0.00538 ( 10) SS BOND : angle 2.83988 ( 20) hydrogen bonds : bond 0.03278 ( 708) hydrogen bonds : angle 4.48874 ( 2265) link_NAG-ASN : bond 0.00599 ( 5) link_NAG-ASN : angle 4.31895 ( 15) *********************** 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 268 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8633 (mmt) cc_final: 0.7792 (mmt) REVERT: A 412 ILE cc_start: 0.7268 (tp) cc_final: 0.6897 (mm) REVERT: B 15 ASP cc_start: 0.7337 (t0) cc_final: 0.7111 (m-30) REVERT: B 103 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8542 (pt0) REVERT: B 140 MET cc_start: 0.7605 (tpp) cc_final: 0.7385 (tpp) REVERT: C 227 MET cc_start: 0.8260 (ppp) cc_final: 0.7458 (ppp) REVERT: C 246 MET cc_start: 0.5187 (tmm) cc_final: 0.4513 (ttm) REVERT: D 223 TYR cc_start: 0.8084 (m-80) cc_final: 0.7760 (m-80) REVERT: E 109 ASP cc_start: 0.5236 (OUTLIER) cc_final: 0.4960 (m-30) REVERT: E 113 TYR cc_start: 0.8247 (t80) cc_final: 0.8042 (t80) REVERT: E 130 ASN cc_start: 0.8005 (t0) cc_final: 0.7801 (t0) REVERT: E 187 ASP cc_start: 0.8353 (m-30) cc_final: 0.7536 (t0) outliers start: 65 outliers final: 55 residues processed: 251 average time/residue: 0.0967 time to fit residues: 38.9325 Evaluate side-chains 253 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 244 ILE 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 103 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 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 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 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 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 129 SER Chi-restraints excluded: chain D residue 189 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 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 157 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 181 SER 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 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 316 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 186 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 = 0.3734 r_free = 0.3734 target = 0.142224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105296 restraints weight = 42200.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111704 restraints weight = 16625.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113698 restraints weight = 8230.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115556 restraints weight = 6190.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115852 restraints weight = 4876.694| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14107 Z= 0.200 Angle : 0.735 12.756 19198 Z= 0.361 Chirality : 0.047 0.349 2185 Planarity : 0.004 0.036 2397 Dihedral : 6.502 59.220 1969 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.36 % Allowed : 25.67 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1687 helix: 2.19 (0.21), residues: 597 sheet: -0.06 (0.28), residues: 354 loop : -1.12 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 174 TYR 0.017 0.002 TYR C 24 PHE 0.021 0.002 PHE B 410 TRP 0.085 0.002 TRP D 239 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00474 (14092) covalent geometry : angle 0.71849 (19163) SS BOND : bond 0.00604 ( 10) SS BOND : angle 2.83487 ( 20) hydrogen bonds : bond 0.03496 ( 708) hydrogen bonds : angle 4.59881 ( 2265) link_NAG-ASN : bond 0.00595 ( 5) link_NAG-ASN : angle 4.62681 ( 15) *********************** 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 272 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8652 (mmt) cc_final: 0.7895 (mmt) REVERT: A 144 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8790 (p0) REVERT: A 153 ILE cc_start: 0.9174 (pt) cc_final: 0.8839 (mt) REVERT: A 156 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 246 MET cc_start: 0.8161 (ppp) cc_final: 0.6836 (ppp) REVERT: C 33 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8043 (mmmt) REVERT: C 188 LEU cc_start: 0.8400 (mt) cc_final: 0.7867 (tp) REVERT: C 227 MET cc_start: 0.8328 (ppp) cc_final: 0.7532 (ppp) REVERT: C 246 MET cc_start: 0.5128 (tmm) cc_final: 0.4680 (ttt) REVERT: E 130 ASN cc_start: 0.8092 (t0) cc_final: 0.7702 (t0) REVERT: E 187 ASP cc_start: 0.8347 (m-30) cc_final: 0.7620 (t0) outliers start: 65 outliers final: 53 residues processed: 258 average time/residue: 0.0995 time to fit residues: 40.8540 Evaluate side-chains 255 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 LEU 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 111 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 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 189 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 290 CYS 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 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 D residue 113 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 298 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 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 181 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106480 restraints weight = 41578.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111558 restraints weight = 16857.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114854 restraints weight = 9450.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116929 restraints weight = 6469.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118166 restraints weight = 5085.559| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14107 Z= 0.157 Angle : 0.718 12.245 19198 Z= 0.349 Chirality : 0.046 0.332 2185 Planarity : 0.004 0.036 2397 Dihedral : 6.482 58.347 1969 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.95 % Allowed : 25.67 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.21), residues: 1687 helix: 2.21 (0.21), residues: 597 sheet: -0.04 (0.28), residues: 353 loop : -1.13 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 174 TYR 0.025 0.001 TYR E 113 PHE 0.020 0.002 PHE E 182 TRP 0.075 0.002 TRP D 239 HIS 0.005 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00361 (14092) covalent geometry : angle 0.70239 (19163) SS BOND : bond 0.00676 ( 10) SS BOND : angle 2.73114 ( 20) hydrogen bonds : bond 0.03332 ( 708) hydrogen bonds : angle 4.57526 ( 2265) link_NAG-ASN : bond 0.00640 ( 5) link_NAG-ASN : angle 4.45600 ( 15) ********************** 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 266 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8645 (mmt) cc_final: 0.7976 (mmt) REVERT: A 144 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8496 (p0) REVERT: A 153 ILE cc_start: 0.9194 (pt) cc_final: 0.8863 (mt) REVERT: A 156 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8127 (mt) REVERT: A 227 MET cc_start: 0.8681 (tpp) cc_final: 0.8299 (mmt) REVERT: A 246 MET cc_start: 0.8148 (ppp) cc_final: 0.6827 (ppp) REVERT: A 415 TRP cc_start: 0.7077 (m-90) cc_final: 0.5977 (m100) REVERT: B 78 TYR cc_start: 0.8268 (m-80) cc_final: 0.8057 (m-80) REVERT: C 33 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8023 (mmmt) REVERT: C 188 LEU cc_start: 0.8401 (mt) cc_final: 0.7899 (tp) REVERT: C 246 MET cc_start: 0.5131 (tmm) cc_final: 0.4794 (ttt) REVERT: E 126 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8271 (tm-30) REVERT: E 130 ASN cc_start: 0.7956 (t0) cc_final: 0.7567 (t0) REVERT: E 187 ASP cc_start: 0.8428 (m-30) cc_final: 0.7794 (t0) outliers start: 59 outliers final: 53 residues processed: 251 average time/residue: 0.1004 time to fit residues: 39.9455 Evaluate side-chains 244 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 LEU 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 18 MET 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 118 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 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 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 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 113 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 298 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 75 THR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 181 SER 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 309 VAL Chi-restraints excluded: chain E residue 312 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 0.0040 chunk 115 optimal weight: 0.0000 chunk 149 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 81 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 186 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 = 0.3794 r_free = 0.3794 target = 0.147522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110009 restraints weight = 44133.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115309 restraints weight = 17393.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118755 restraints weight = 9612.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120863 restraints weight = 6495.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122343 restraints weight = 5086.589| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.8064 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= 0.125 Angle : 0.693 11.331 19198 Z= 0.334 Chirality : 0.045 0.295 2185 Planarity : 0.003 0.036 2397 Dihedral : 6.385 59.988 1969 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 3.35 % Allowed : 26.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.21), residues: 1687 helix: 2.33 (0.21), residues: 591 sheet: 0.04 (0.28), residues: 350 loop : -1.02 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 174 TYR 0.022 0.001 TYR E 113 PHE 0.017 0.001 PHE A 44 TRP 0.049 0.002 TRP C 239 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00271 (14092) covalent geometry : angle 0.67908 (19163) SS BOND : bond 0.00577 ( 10) SS BOND : angle 2.59800 ( 20) hydrogen bonds : bond 0.03149 ( 708) hydrogen bonds : angle 4.47452 ( 2265) link_NAG-ASN : bond 0.00642 ( 5) link_NAG-ASN : angle 4.01296 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.91 seconds wall clock time: 44 minutes 3.10 seconds (2643.10 seconds total)