Starting phenix.real_space_refine on Fri Mar 6 14:43:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5m_21543/03_2026/6w5m_21543.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5m_21543/03_2026/6w5m_21543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5m_21543/03_2026/6w5m_21543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5m_21543/03_2026/6w5m_21543.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5m_21543/03_2026/6w5m_21543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5m_21543/03_2026/6w5m_21543.cif" } resolution = 4.6 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15451 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 58 5.16 5 C 11457 2.51 5 N 3551 2.21 5 O 4216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19574 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2381 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain: "B" Number of atoms: 2302 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 2299 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 298, 2299 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2351 Chain: "C" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1185 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1742 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain breaks: 1 Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 4.67, per 1000 atoms: 0.24 Number of scatterers: 19574 At special positions: 0 Unit cell: (143, 121, 134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 292 15.00 O 4216 8.00 N 3551 7.00 C 11457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 620.8 milliseconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 35.6% alpha, 21.1% beta 156 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 3815 through 3830 removed outlier: 5.141A pdb=" N LYS C3828 " --> pdb=" O LYS C3824 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU C3829 " --> pdb=" O LYS C3825 " (cutoff:3.500A) Processing helix chain 'C' and resid 3867 through 3879 Processing helix chain 'C' and resid 3901 through 3905 removed outlier: 3.523A pdb=" N ILE C3905 " --> pdb=" O ALA C3902 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.804A pdb=" N ARG D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 524 removed outlier: 3.573A pdb=" N MET D 503 " --> pdb=" O PRO D 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.664A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.586A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.892A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.926A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.524A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.538A pdb=" N LYS J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.664A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.585A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.892A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.924A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.523A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.662A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.936A pdb=" N THR A 29 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 3.780A pdb=" N SER A 71 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 90 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN A 92 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 116 removed outlier: 6.543A pdb=" N CYS A 126 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 113 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 124 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR A 115 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS A 122 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 159 removed outlier: 4.504A pdb=" N LYS A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.144A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 303 removed outlier: 6.528A pdb=" N ILE A 313 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 301 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA A 311 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 42 removed outlier: 5.425A pdb=" N LEU B 37 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS B 331 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 39 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 326 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.542A pdb=" N SER B 64 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY B 73 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 79 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 95 removed outlier: 3.890A pdb=" N THR B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP B 115 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 121 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.438A pdb=" N VAL B 153 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 166 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 155 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.910A pdb=" N CYS B 195 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP B 199 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N CYS B 205 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 217 through 222 removed outlier: 3.564A pdb=" N PHE B 219 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 238 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 251 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 240 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.851A pdb=" N VAL B 283 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 296 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 285 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3831 through 3835 Processing sheet with id=AB7, first strand: chain 'C' and resid 3854 through 3857 removed outlier: 7.067A pdb=" N MET C3854 " --> pdb=" O ALA C3930 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C3930 " --> pdb=" O MET C3854 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3860 through 3864 Processing sheet with id=AB9, first strand: chain 'C' and resid 3906 through 3907 removed outlier: 6.904A pdb=" N ASN C3906 " --> pdb=" O TYR C3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 298 through 301 Processing sheet with id=AC2, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.931A pdb=" N THR D 372 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 454 through 460 removed outlier: 5.951A pdb=" N PHE D 449 " --> pdb=" O GLN D 456 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL D 458 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE D 447 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 479 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.363A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.182A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 77 through 78 removed outlier: 3.755A pdb=" N ILE I 78 " --> pdb=" O GLY J 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.405A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.259A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 77 through 78 652 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 396 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4830 1.33 - 1.45: 5417 1.45 - 1.57: 9654 1.57 - 1.69: 582 1.69 - 1.81: 82 Bond restraints: 20565 Sorted by residual: bond pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.83e+00 bond pdb=" C3' DC P 126 " pdb=" O3' DC P 126 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" C4' DG P 112 " pdb=" O4' DG P 112 " ideal model delta sigma weight residual 1.450 1.476 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C PRO D 530 " pdb=" N PRO D 531 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.61e+00 bond pdb=" C1' DC O 96 " pdb=" N1 DC O 96 " ideal model delta sigma weight residual 1.490 1.453 0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 20560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 28874 2.65 - 5.29: 184 5.29 - 7.94: 12 7.94 - 10.58: 0 10.58 - 13.23: 2 Bond angle restraints: 29072 Sorted by residual: angle pdb=" N ILE A 66 " pdb=" CA ILE A 66 " pdb=" C ILE A 66 " ideal model delta sigma weight residual 112.35 104.62 7.73 1.41e+00 5.03e-01 3.01e+01 angle pdb=" CA ILE A 66 " pdb=" C ILE A 66 " pdb=" N HIS A 67 " ideal model delta sigma weight residual 117.99 113.91 4.08 1.22e+00 6.72e-01 1.12e+01 angle pdb=" CA TRP D 505 " pdb=" CB TRP D 505 " pdb=" CG TRP D 505 " ideal model delta sigma weight residual 113.60 119.08 -5.48 1.90e+00 2.77e-01 8.31e+00 angle pdb=" N GLY D 485 " pdb=" CA GLY D 485 " pdb=" C GLY D 485 " ideal model delta sigma weight residual 112.34 117.97 -5.63 2.04e+00 2.40e-01 7.61e+00 angle pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " pdb=" P DC P 16 " ideal model delta sigma weight residual 120.20 124.31 -4.11 1.50e+00 4.44e-01 7.50e+00 ... (remaining 29067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 9946 35.18 - 70.37: 1546 70.37 - 105.55: 44 105.55 - 140.74: 3 140.74 - 175.92: 2 Dihedral angle restraints: 11541 sinusoidal: 6537 harmonic: 5004 Sorted by residual: dihedral pdb=" CA PRO D 531 " pdb=" C PRO D 531 " pdb=" N TRP D 532 " pdb=" CA TRP D 532 " ideal model delta harmonic sigma weight residual -180.00 -149.89 -30.11 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA ASN L 64 " pdb=" C ASN L 64 " pdb=" N VAL L 65 " pdb=" CA VAL L 65 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASN H 64 " pdb=" C ASN H 64 " pdb=" N VAL H 65 " pdb=" CA VAL H 65 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 11538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2756 0.057 - 0.115: 475 0.115 - 0.172: 42 0.172 - 0.230: 5 0.230 - 0.287: 1 Chirality restraints: 3279 Sorted by residual: chirality pdb=" CA ILE A 66 " pdb=" N ILE A 66 " pdb=" C ILE A 66 " pdb=" CB ILE A 66 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU K 100 " pdb=" CB LEU K 100 " pdb=" CD1 LEU K 100 " pdb=" CD2 LEU K 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CG LEU H 58 " pdb=" CB LEU H 58 " pdb=" CD1 LEU H 58 " pdb=" CD2 LEU H 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 3276 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 485 " 0.051 5.00e-02 4.00e+02 7.75e-02 9.61e+00 pdb=" N PRO D 486 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 486 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 486 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 531 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C PRO D 531 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO D 531 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP D 532 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 54 " 0.002 2.00e-02 2.50e+03 1.54e-02 5.30e+00 pdb=" N1 DC O 54 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DC O 54 " 0.039 2.00e-02 2.50e+03 pdb=" O2 DC O 54 " -0.021 2.00e-02 2.50e+03 pdb=" N3 DC O 54 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC O 54 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC O 54 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC O 54 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC O 54 " -0.002 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 216 2.45 - 3.06: 13837 3.06 - 3.67: 38477 3.67 - 4.29: 52484 4.29 - 4.90: 75713 Nonbonded interactions: 180727 Sorted by model distance: nonbonded pdb=" OG1 THR N 29 " pdb=" OP1 DT O 104 " model vdw 1.832 3.040 nonbonded pdb=" O GLU L 74 " pdb=" NH2 ARG N 89 " model vdw 1.961 3.120 nonbonded pdb=" NH1 ARG M 29 " pdb=" O SER N 33 " model vdw 1.996 3.120 nonbonded pdb=" CE LYS G 122 " pdb=" NZ LYS K 115 " model vdw 2.060 3.520 nonbonded pdb=" NH2 ARG I 77 " pdb=" O4' DA O 131 " model vdw 2.070 3.120 ... (remaining 180722 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 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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=0.50 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.540 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.005 0.050 20565 Z= 0.262 Angle : 0.682 13.229 29072 Z= 0.400 Chirality : 0.043 0.287 3279 Planarity : 0.005 0.078 2665 Dihedral : 25.405 175.923 8321 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 36.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.58 % Allowed : 6.66 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -2.98 (0.18), residues: 1699 helix: -1.56 (0.19), residues: 578 sheet: -1.88 (0.24), residues: 373 loop : -2.25 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 42 TYR 0.016 0.002 TYR J 118 PHE 0.019 0.002 PHE D 484 TRP 0.021 0.002 TRP D 505 HIS 0.005 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00543 (20565) covalent geometry : angle 0.68241 (29072) hydrogen bonds : bond 0.19512 ( 1048) hydrogen bonds : angle 6.55139 ( 2646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 533 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.1024 (t0) cc_final: 0.0770 (m-30) REVERT: A 80 LYS cc_start: 0.1410 (mmtt) cc_final: 0.0941 (mtmt) REVERT: A 137 LEU cc_start: 0.3783 (mt) cc_final: 0.3390 (mm) REVERT: A 213 PHE cc_start: 0.5150 (p90) cc_final: 0.4770 (p90) REVERT: A 247 ASP cc_start: 0.0822 (t0) cc_final: 0.0609 (t0) REVERT: C 3931 MET cc_start: -0.0630 (mtp) cc_final: -0.1033 (ttp) REVERT: D 288 LEU cc_start: 0.6546 (mt) cc_final: 0.6302 (mt) REVERT: D 336 MET cc_start: 0.4982 (tmm) cc_final: 0.3638 (mmt) REVERT: G 58 THR cc_start: 0.8511 (m) cc_final: 0.8165 (p) REVERT: G 65 LEU cc_start: 0.9331 (mt) cc_final: 0.8893 (mm) REVERT: G 73 GLU cc_start: 0.8546 (tt0) cc_final: 0.8237 (tm-30) REVERT: G 74 ILE cc_start: 0.9396 (mm) cc_final: 0.9190 (mm) REVERT: G 97 GLU cc_start: 0.9206 (mt-10) cc_final: 0.7136 (mt-10) REVERT: H 44 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8095 (mtmt) REVERT: H 67 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8270 (tmm-80) REVERT: I 32 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8348 (tpt170) REVERT: I 56 GLU cc_start: 0.9256 (tt0) cc_final: 0.8851 (tt0) REVERT: I 65 LEU cc_start: 0.9203 (mt) cc_final: 0.8887 (mt) REVERT: I 92 GLU cc_start: 0.8658 (mt-10) cc_final: 0.6028 (mt-10) REVERT: J 38 VAL cc_start: 0.9625 (m) cc_final: 0.9205 (m) REVERT: J 59 MET cc_start: 0.9238 (mmm) cc_final: 0.9024 (mmp) REVERT: J 96 ARG cc_start: 0.9142 (mtp180) cc_final: 0.8839 (ttm170) REVERT: J 103 LEU cc_start: 0.9424 (mt) cc_final: 0.8908 (mt) REVERT: K 59 GLU cc_start: 0.8256 (pm20) cc_final: 0.8024 (pm20) REVERT: K 73 GLU cc_start: 0.8644 (tt0) cc_final: 0.8438 (mt-10) REVERT: K 82 LEU cc_start: 0.8648 (mt) cc_final: 0.8448 (mm) REVERT: K 84 PHE cc_start: 0.8293 (m-80) cc_final: 0.7703 (m-80) REVERT: K 94 GLU cc_start: 0.9175 (tp30) cc_final: 0.8929 (tp30) REVERT: K 105 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8865 (tm-30) REVERT: L 51 TYR cc_start: 0.7804 (m-10) cc_final: 0.7375 (m-10) REVERT: L 66 ILE cc_start: 0.9659 (mp) cc_final: 0.9354 (tt) REVERT: M 23 LEU cc_start: 0.8292 (mt) cc_final: 0.7881 (mt) REVERT: M 56 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8167 (mt-10) REVERT: M 57 TYR cc_start: 0.9008 (t80) cc_final: 0.8280 (t80) REVERT: M 61 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8871 (mm-30) REVERT: M 65 LEU cc_start: 0.9414 (mt) cc_final: 0.9038 (mt) REVERT: M 68 ASN cc_start: 0.7909 (m-40) cc_final: 0.7538 (m-40) REVERT: M 87 VAL cc_start: 0.8959 (t) cc_final: 0.8495 (t) REVERT: M 88 ARG cc_start: 0.9060 (mmt180) cc_final: 0.8792 (mmp80) REVERT: M 90 ASP cc_start: 0.9080 (t0) cc_final: 0.8842 (t0) REVERT: M 91 GLU cc_start: 0.8622 (pm20) cc_final: 0.8043 (tm-30) REVERT: N 65 ASP cc_start: 0.9012 (t0) cc_final: 0.8653 (t0) REVERT: N 91 ILE cc_start: 0.9062 (mm) cc_final: 0.8725 (mm) REVERT: N 92 GLN cc_start: 0.8888 (tt0) cc_final: 0.8450 (tm-30) REVERT: N 117 LYS cc_start: 0.7177 (tttm) cc_final: 0.6796 (tttp) outliers start: 23 outliers final: 6 residues processed: 537 average time/residue: 0.1891 time to fit residues: 142.7315 Evaluate side-chains 356 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 349 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN B 178 HIS ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 287 ASN B 289 GLN B 310 HIS C3839 HIS G 39 HIS G 76 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN J 60 ASN J 92 GLN J 106 HIS K 68 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN M 31 HIS ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN N 46 HIS ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.112268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.070638 restraints weight = 90884.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.072675 restraints weight = 46066.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073907 restraints weight = 29635.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074696 restraints weight = 22337.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.075177 restraints weight = 18896.512| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.177 20565 Z= 0.283 Angle : 0.734 7.242 29072 Z= 0.412 Chirality : 0.045 0.227 3279 Planarity : 0.007 0.062 2665 Dihedral : 29.654 176.932 5081 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % 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 are not related in a simple way. whole: -1.57 (0.19), residues: 1699 helix: 0.08 (0.20), residues: 591 sheet: -1.30 (0.25), residues: 377 loop : -1.78 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG M 32 TYR 0.024 0.002 TYR M 39 PHE 0.029 0.003 PHE G 67 TRP 0.023 0.002 TRP D 505 HIS 0.007 0.002 HIS J 46 Details of bonding type rmsd covalent geometry : bond 0.00618 (20565) covalent geometry : angle 0.73440 (29072) hydrogen bonds : bond 0.08638 ( 1048) hydrogen bonds : angle 5.01970 ( 2646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 417 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.1389 (t0) cc_final: 0.0950 (m-30) REVERT: A 80 LYS cc_start: 0.0840 (mmtt) cc_final: 0.0433 (mtmt) REVERT: A 134 MET cc_start: -0.1056 (mtm) cc_final: -0.1297 (mtm) REVERT: A 213 PHE cc_start: 0.5128 (p90) cc_final: 0.4199 (p90) REVERT: C 3883 TYR cc_start: 0.4897 (m-80) cc_final: 0.4620 (m-80) REVERT: C 3884 MET cc_start: 0.2188 (ttp) cc_final: 0.1505 (tmm) REVERT: C 3931 MET cc_start: -0.0524 (mtp) cc_final: -0.1118 (ttt) REVERT: D 336 MET cc_start: 0.4019 (tmm) cc_final: 0.3548 (mmt) REVERT: D 337 PRO cc_start: 0.2481 (Cg_exo) cc_final: 0.1823 (Cg_endo) REVERT: D 518 TYR cc_start: -0.2057 (t80) cc_final: -0.2321 (m-10) REVERT: G 55 GLN cc_start: 0.8899 (mt0) cc_final: 0.8339 (mt0) REVERT: G 61 LEU cc_start: 0.8449 (mm) cc_final: 0.8084 (mm) REVERT: G 97 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8244 (mt-10) REVERT: G 120 MET cc_start: 0.8453 (tpt) cc_final: 0.8062 (mmm) REVERT: H 27 GLN cc_start: 0.8847 (pp30) cc_final: 0.8362 (pp30) REVERT: H 64 ASN cc_start: 0.9232 (m-40) cc_final: 0.8665 (m-40) REVERT: H 65 VAL cc_start: 0.9786 (m) cc_final: 0.9261 (p) REVERT: H 67 ARG cc_start: 0.9311 (ttp-110) cc_final: 0.8817 (ttp80) REVERT: H 68 ASP cc_start: 0.9228 (m-30) cc_final: 0.8813 (p0) REVERT: H 75 HIS cc_start: 0.8260 (t-90) cc_final: 0.7943 (t-90) REVERT: H 84 MET cc_start: 0.8995 (mmm) cc_final: 0.8730 (mmm) REVERT: H 88 TYR cc_start: 0.8890 (m-10) cc_final: 0.8530 (m-10) REVERT: I 38 ASN cc_start: 0.9245 (m110) cc_final: 0.8980 (m-40) REVERT: I 64 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8479 (tm-30) REVERT: I 90 ASP cc_start: 0.9005 (t0) cc_final: 0.8708 (t0) REVERT: I 92 GLU cc_start: 0.8217 (mt-10) cc_final: 0.6528 (mt-10) REVERT: I 99 ARG cc_start: 0.9030 (ptp90) cc_final: 0.8810 (mtm-85) REVERT: I 102 ILE cc_start: 0.9524 (tp) cc_final: 0.9165 (tp) REVERT: J 59 MET cc_start: 0.8946 (mmm) cc_final: 0.8681 (mmm) REVERT: J 96 ARG cc_start: 0.9000 (mtp180) cc_final: 0.8679 (ttm110) REVERT: J 97 LEU cc_start: 0.9493 (tt) cc_final: 0.9202 (tt) REVERT: J 103 LEU cc_start: 0.9399 (mt) cc_final: 0.8612 (mt) REVERT: J 106 HIS cc_start: 0.8588 (m90) cc_final: 0.7967 (m170) REVERT: K 51 ILE cc_start: 0.9291 (mt) cc_final: 0.9056 (mm) REVERT: K 73 GLU cc_start: 0.8498 (tt0) cc_final: 0.7996 (tt0) REVERT: K 77 ASP cc_start: 0.9287 (t0) cc_final: 0.9074 (t70) REVERT: K 80 THR cc_start: 0.8312 (p) cc_final: 0.7674 (p) REVERT: K 81 ASP cc_start: 0.8541 (m-30) cc_final: 0.8161 (m-30) REVERT: K 84 PHE cc_start: 0.8664 (m-80) cc_final: 0.8288 (m-80) REVERT: K 85 GLN cc_start: 0.8876 (mp-120) cc_final: 0.8411 (mm110) REVERT: K 90 MET cc_start: 0.9166 (mmm) cc_final: 0.8963 (mmm) REVERT: K 93 GLN cc_start: 0.8947 (pp30) cc_final: 0.7671 (pp30) REVERT: K 94 GLU cc_start: 0.8987 (tp30) cc_final: 0.8601 (tp30) REVERT: K 120 MET cc_start: 0.8791 (tpp) cc_final: 0.8578 (mmm) REVERT: K 122 LYS cc_start: 0.8833 (pttp) cc_final: 0.8221 (pttt) REVERT: K 125 GLN cc_start: 0.9252 (pt0) cc_final: 0.8737 (pp30) REVERT: L 25 ASN cc_start: 0.8600 (m110) cc_final: 0.7663 (m110) REVERT: L 37 LEU cc_start: 0.9397 (mt) cc_final: 0.9000 (mt) REVERT: L 45 ARG cc_start: 0.8986 (tpp80) cc_final: 0.8163 (tpp80) REVERT: L 66 ILE cc_start: 0.9713 (OUTLIER) cc_final: 0.9360 (tt) REVERT: L 75 HIS cc_start: 0.8969 (t-90) cc_final: 0.8689 (t-170) REVERT: L 85 ASP cc_start: 0.9047 (m-30) cc_final: 0.8832 (m-30) REVERT: M 68 ASN cc_start: 0.7945 (m-40) cc_final: 0.7610 (m110) REVERT: M 87 VAL cc_start: 0.9135 (t) cc_final: 0.8926 (t) REVERT: M 88 ARG cc_start: 0.9317 (mmt180) cc_final: 0.9096 (mmp80) REVERT: M 100 VAL cc_start: 0.9497 (t) cc_final: 0.9182 (t) REVERT: M 108 LEU cc_start: 0.9342 (pt) cc_final: 0.9081 (pt) REVERT: N 48 ASP cc_start: 0.8497 (p0) cc_final: 0.8214 (t0) REVERT: N 68 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8227 (mm-30) REVERT: N 76 ARG cc_start: 0.9163 (ttm-80) cc_final: 0.8892 (ttm-80) REVERT: N 81 ASN cc_start: 0.8694 (t0) cc_final: 0.8267 (t0) REVERT: N 92 GLN cc_start: 0.9090 (tt0) cc_final: 0.8542 (tm-30) outliers start: 3 outliers final: 0 residues processed: 418 average time/residue: 0.1727 time to fit residues: 104.5205 Evaluate side-chains 328 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 160 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN G 76 GLN G 93 GLN J 92 GLN K 68 GLN K 85 GLN ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 ASN ** 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 = 0.3978 r_free = 0.3978 target = 0.110252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068956 restraints weight = 90564.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071129 restraints weight = 45110.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.072387 restraints weight = 28471.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073119 restraints weight = 21217.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073528 restraints weight = 17733.062| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 20565 Z= 0.290 Angle : 0.717 10.217 29072 Z= 0.401 Chirality : 0.045 0.304 3279 Planarity : 0.006 0.060 2665 Dihedral : 29.639 177.423 5081 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1699 helix: 0.45 (0.20), residues: 587 sheet: -1.15 (0.26), residues: 374 loop : -1.50 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 92 TYR 0.021 0.002 TYR M 39 PHE 0.028 0.002 PHE G 67 TRP 0.022 0.002 TRP D 505 HIS 0.010 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00634 (20565) covalent geometry : angle 0.71690 (29072) hydrogen bonds : bond 0.08647 ( 1048) hydrogen bonds : angle 4.83635 ( 2646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.1136 (mmtt) cc_final: 0.0625 (mtmt) REVERT: A 213 PHE cc_start: 0.5004 (p90) cc_final: 0.4224 (p90) REVERT: C 3883 TYR cc_start: 0.4797 (m-80) cc_final: 0.4410 (m-80) REVERT: C 3931 MET cc_start: -0.0498 (mtp) cc_final: -0.1111 (ttt) REVERT: D 293 ASP cc_start: 0.4540 (t0) cc_final: 0.4320 (t0) REVERT: D 327 TRP cc_start: 0.7792 (p-90) cc_final: 0.7528 (p-90) REVERT: D 336 MET cc_start: 0.3710 (tmm) cc_final: 0.3184 (mmt) REVERT: G 55 GLN cc_start: 0.8837 (mt0) cc_final: 0.8166 (mt0) REVERT: G 65 LEU cc_start: 0.9445 (mm) cc_final: 0.9196 (mm) REVERT: G 119 ILE cc_start: 0.8478 (pt) cc_final: 0.7382 (pt) REVERT: G 120 MET cc_start: 0.8329 (tpt) cc_final: 0.8056 (mmp) REVERT: G 130 ILE cc_start: 0.9453 (mm) cc_final: 0.9103 (mm) REVERT: H 27 GLN cc_start: 0.8910 (pp30) cc_final: 0.8658 (pp30) REVERT: H 44 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8660 (tppt) REVERT: H 63 GLU cc_start: 0.8923 (tp30) cc_final: 0.8444 (tp30) REVERT: H 67 ARG cc_start: 0.9336 (ttp-110) cc_final: 0.8768 (ttm110) REVERT: H 74 GLU cc_start: 0.8010 (tp30) cc_final: 0.7780 (tp30) REVERT: H 75 HIS cc_start: 0.8242 (t-90) cc_final: 0.7919 (t-90) REVERT: H 84 MET cc_start: 0.8726 (mmm) cc_final: 0.8521 (mmm) REVERT: H 88 TYR cc_start: 0.8977 (m-10) cc_final: 0.8574 (m-10) REVERT: I 38 ASN cc_start: 0.9325 (m110) cc_final: 0.9082 (m110) REVERT: I 64 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8577 (tm-30) REVERT: I 90 ASP cc_start: 0.9084 (t0) cc_final: 0.8643 (t0) REVERT: I 91 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8803 (tm-30) REVERT: I 92 GLU cc_start: 0.8042 (mt-10) cc_final: 0.6605 (mt-10) REVERT: J 37 TYR cc_start: 0.8956 (m-80) cc_final: 0.8725 (m-80) REVERT: J 92 GLN cc_start: 0.9219 (pt0) cc_final: 0.8969 (pt0) REVERT: J 96 ARG cc_start: 0.9089 (mtp180) cc_final: 0.8841 (ttm110) REVERT: J 103 LEU cc_start: 0.9447 (mt) cc_final: 0.8969 (mt) REVERT: J 106 HIS cc_start: 0.8581 (m90) cc_final: 0.8344 (m-70) REVERT: K 73 GLU cc_start: 0.8328 (tt0) cc_final: 0.7639 (tt0) REVERT: K 80 THR cc_start: 0.8417 (p) cc_final: 0.7599 (p) REVERT: K 81 ASP cc_start: 0.8423 (m-30) cc_final: 0.8148 (m-30) REVERT: K 84 PHE cc_start: 0.8666 (m-80) cc_final: 0.8251 (m-80) REVERT: K 85 GLN cc_start: 0.9165 (mp10) cc_final: 0.8582 (mm110) REVERT: K 105 GLU cc_start: 0.9213 (tt0) cc_final: 0.8885 (pp20) REVERT: K 117 VAL cc_start: 0.9250 (m) cc_final: 0.8928 (p) REVERT: K 122 LYS cc_start: 0.8811 (pttp) cc_final: 0.8588 (pttt) REVERT: K 125 GLN cc_start: 0.9145 (pt0) cc_final: 0.8537 (pp30) REVERT: L 25 ASN cc_start: 0.8506 (m110) cc_final: 0.7673 (m110) REVERT: L 39 ARG cc_start: 0.9169 (mmt180) cc_final: 0.8823 (mmm160) REVERT: L 63 GLU cc_start: 0.8786 (tp30) cc_final: 0.8421 (tm-30) REVERT: L 84 MET cc_start: 0.8702 (mpp) cc_final: 0.8309 (mmm) REVERT: L 88 TYR cc_start: 0.8421 (m-80) cc_final: 0.7749 (m-80) REVERT: L 98 TYR cc_start: 0.8466 (m-10) cc_final: 0.8135 (m-80) REVERT: M 57 TYR cc_start: 0.9086 (t80) cc_final: 0.7695 (t80) REVERT: M 64 GLU cc_start: 0.9097 (pp20) cc_final: 0.8607 (pp20) REVERT: M 65 LEU cc_start: 0.9604 (mt) cc_final: 0.9273 (mt) REVERT: M 68 ASN cc_start: 0.8687 (m-40) cc_final: 0.7999 (m110) REVERT: M 87 VAL cc_start: 0.9297 (t) cc_final: 0.8933 (t) REVERT: M 92 GLU cc_start: 0.8817 (tt0) cc_final: 0.8496 (tt0) REVERT: M 95 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8773 (ttmt) REVERT: M 108 LEU cc_start: 0.9520 (pt) cc_final: 0.9197 (pt) REVERT: N 59 MET cc_start: 0.9207 (mmp) cc_final: 0.8998 (mmp) REVERT: N 65 ASP cc_start: 0.8847 (t0) cc_final: 0.8562 (t0) REVERT: N 68 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8165 (mm-30) REVERT: N 76 ARG cc_start: 0.9224 (ttm-80) cc_final: 0.8927 (ttm-80) REVERT: N 92 GLN cc_start: 0.9181 (tt0) cc_final: 0.8791 (tm-30) outliers start: 2 outliers final: 0 residues processed: 389 average time/residue: 0.1653 time to fit residues: 94.9893 Evaluate side-chains 324 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 34 optimal weight: 0.4980 chunk 189 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN H 25 ASN J 92 GLN K 68 GLN K 108 ASN L 27 GLN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 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 = 0.3987 r_free = 0.3987 target = 0.111351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070267 restraints weight = 91513.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072413 restraints weight = 45705.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.073779 restraints weight = 28867.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074661 restraints weight = 21352.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075150 restraints weight = 17673.489| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 20565 Z= 0.211 Angle : 0.667 10.758 29072 Z= 0.374 Chirality : 0.043 0.204 3279 Planarity : 0.006 0.104 2665 Dihedral : 29.514 178.330 5081 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % 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 are not related in a simple way. whole: -0.90 (0.19), residues: 1699 helix: 0.69 (0.20), residues: 600 sheet: -0.94 (0.26), residues: 361 loop : -1.45 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 190 TYR 0.026 0.002 TYR H 98 PHE 0.021 0.002 PHE G 67 TRP 0.024 0.002 TRP D 505 HIS 0.008 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00463 (20565) covalent geometry : angle 0.66739 (29072) hydrogen bonds : bond 0.07793 ( 1048) hydrogen bonds : angle 4.52815 ( 2646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.1002 (mm) cc_final: 0.0453 (pt) REVERT: A 80 LYS cc_start: 0.1120 (mmtt) cc_final: 0.0643 (mtmt) REVERT: A 213 PHE cc_start: 0.4935 (p90) cc_final: 0.4261 (p90) REVERT: C 3883 TYR cc_start: 0.4753 (m-80) cc_final: 0.4336 (m-80) REVERT: C 3931 MET cc_start: -0.0717 (mtp) cc_final: -0.1325 (ttt) REVERT: D 336 MET cc_start: 0.4494 (tmm) cc_final: 0.2963 (mmt) REVERT: G 48 LEU cc_start: 0.9680 (tt) cc_final: 0.9410 (pp) REVERT: G 55 GLN cc_start: 0.8897 (mt0) cc_final: 0.8338 (mt0) REVERT: G 61 LEU cc_start: 0.9169 (mm) cc_final: 0.8910 (mt) REVERT: G 104 PHE cc_start: 0.9480 (m-80) cc_final: 0.9235 (m-80) REVERT: G 119 ILE cc_start: 0.8601 (pt) cc_final: 0.7453 (pt) REVERT: G 120 MET cc_start: 0.8276 (tpt) cc_final: 0.7958 (mmp) REVERT: H 27 GLN cc_start: 0.8922 (pp30) cc_final: 0.8620 (pp30) REVERT: H 29 ILE cc_start: 0.9475 (mm) cc_final: 0.9219 (pt) REVERT: H 44 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8478 (tppt) REVERT: H 63 GLU cc_start: 0.8994 (tp30) cc_final: 0.8289 (tp30) REVERT: H 67 ARG cc_start: 0.9353 (ttp-110) cc_final: 0.8621 (ttm110) REVERT: H 68 ASP cc_start: 0.9272 (m-30) cc_final: 0.8672 (p0) REVERT: H 73 THR cc_start: 0.9722 (m) cc_final: 0.9478 (p) REVERT: H 74 GLU cc_start: 0.7954 (tp30) cc_final: 0.7666 (tp30) REVERT: H 88 TYR cc_start: 0.9005 (m-10) cc_final: 0.8774 (m-80) REVERT: I 38 ASN cc_start: 0.9299 (m110) cc_final: 0.9045 (m110) REVERT: I 64 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8556 (tm-30) REVERT: I 84 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8689 (tp-100) REVERT: I 90 ASP cc_start: 0.8991 (t0) cc_final: 0.8530 (t0) REVERT: I 104 GLN cc_start: 0.8755 (mp10) cc_final: 0.8270 (mp10) REVERT: J 34 TYR cc_start: 0.9427 (m-80) cc_final: 0.9181 (m-10) REVERT: J 92 GLN cc_start: 0.9254 (pt0) cc_final: 0.9015 (pt0) REVERT: J 96 ARG cc_start: 0.9046 (mtp180) cc_final: 0.8734 (ttm110) REVERT: K 73 GLU cc_start: 0.8275 (tt0) cc_final: 0.7728 (tt0) REVERT: K 84 PHE cc_start: 0.8706 (m-80) cc_final: 0.8326 (m-80) REVERT: K 85 GLN cc_start: 0.9229 (mp10) cc_final: 0.8932 (mm110) REVERT: K 97 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8512 (mt-10) REVERT: K 99 TYR cc_start: 0.8568 (t80) cc_final: 0.8248 (t80) REVERT: K 105 GLU cc_start: 0.9259 (tt0) cc_final: 0.8915 (pp20) REVERT: K 117 VAL cc_start: 0.9340 (m) cc_final: 0.9033 (p) REVERT: K 125 GLN cc_start: 0.9130 (pt0) cc_final: 0.8550 (pp30) REVERT: L 22 LEU cc_start: 0.8288 (mm) cc_final: 0.7795 (mm) REVERT: L 25 ASN cc_start: 0.8525 (m110) cc_final: 0.7654 (m110) REVERT: L 45 ARG cc_start: 0.9069 (tpp80) cc_final: 0.8789 (tpp80) REVERT: L 63 GLU cc_start: 0.8691 (tp30) cc_final: 0.7839 (tm-30) REVERT: L 72 TYR cc_start: 0.9283 (m-10) cc_final: 0.8714 (m-10) REVERT: L 75 HIS cc_start: 0.9153 (t-90) cc_final: 0.8835 (t-170) REVERT: L 84 MET cc_start: 0.8662 (mpp) cc_final: 0.8376 (mmm) REVERT: L 85 ASP cc_start: 0.9142 (m-30) cc_final: 0.8649 (m-30) REVERT: L 88 TYR cc_start: 0.8561 (m-80) cc_final: 0.7944 (m-80) REVERT: L 98 TYR cc_start: 0.8724 (m-10) cc_final: 0.8371 (m-80) REVERT: M 57 TYR cc_start: 0.9009 (t80) cc_final: 0.8048 (t80) REVERT: M 64 GLU cc_start: 0.9125 (pp20) cc_final: 0.8838 (pp20) REVERT: M 72 ASP cc_start: 0.8574 (m-30) cc_final: 0.8000 (t70) REVERT: M 84 GLN cc_start: 0.9361 (tp-100) cc_final: 0.8955 (tp-100) REVERT: M 95 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8775 (ttmt) REVERT: M 108 LEU cc_start: 0.9555 (pt) cc_final: 0.9237 (pt) REVERT: N 65 ASP cc_start: 0.8850 (t0) cc_final: 0.8621 (t0) REVERT: N 69 ARG cc_start: 0.9232 (ttm170) cc_final: 0.8625 (ttm110) REVERT: N 81 ASN cc_start: 0.9235 (t0) cc_final: 0.8925 (t0) REVERT: N 92 GLN cc_start: 0.9257 (tt0) cc_final: 0.8631 (tm-30) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.1572 time to fit residues: 89.0574 Evaluate side-chains 315 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 78 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 134 optimal weight: 0.0060 chunk 125 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN H 64 ASN J 46 HIS J 79 HIS K 68 GLN M 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.108537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067811 restraints weight = 92675.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069939 restraints weight = 46549.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071270 restraints weight = 29476.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072106 restraints weight = 21790.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072533 restraints weight = 18108.139| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 20565 Z= 0.289 Angle : 0.714 9.644 29072 Z= 0.401 Chirality : 0.044 0.220 3279 Planarity : 0.006 0.104 2665 Dihedral : 29.540 178.091 5081 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 are not related in a simple way. whole: -0.89 (0.19), residues: 1699 helix: 0.63 (0.20), residues: 584 sheet: -0.70 (0.27), residues: 353 loop : -1.48 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 39 TYR 0.030 0.002 TYR L 51 PHE 0.019 0.002 PHE G 67 TRP 0.023 0.002 TRP D 505 HIS 0.022 0.002 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00635 (20565) covalent geometry : angle 0.71390 (29072) hydrogen bonds : bond 0.08617 ( 1048) hydrogen bonds : angle 4.74079 ( 2646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.0897 (mm) cc_final: 0.0324 (pt) REVERT: A 80 LYS cc_start: 0.1179 (mmtt) cc_final: 0.0721 (mtmt) REVERT: A 213 PHE cc_start: 0.4925 (p90) cc_final: 0.4323 (p90) REVERT: C 3883 TYR cc_start: 0.4593 (m-80) cc_final: 0.4296 (m-80) REVERT: C 3931 MET cc_start: -0.0553 (mtp) cc_final: -0.1131 (ttt) REVERT: D 336 MET cc_start: 0.4299 (tmm) cc_final: 0.3089 (mmt) REVERT: G 55 GLN cc_start: 0.8918 (mt0) cc_final: 0.8326 (mt0) REVERT: G 61 LEU cc_start: 0.9100 (mm) cc_final: 0.8747 (mt) REVERT: G 65 LEU cc_start: 0.9473 (mm) cc_final: 0.9216 (mm) REVERT: G 119 ILE cc_start: 0.8633 (pt) cc_final: 0.7270 (pt) REVERT: G 120 MET cc_start: 0.8439 (tpt) cc_final: 0.8052 (mmp) REVERT: H 27 GLN cc_start: 0.8985 (pp30) cc_final: 0.8689 (pp30) REVERT: H 29 ILE cc_start: 0.9523 (mm) cc_final: 0.9167 (pt) REVERT: H 44 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8860 (tppt) REVERT: H 63 GLU cc_start: 0.9016 (tp30) cc_final: 0.8654 (tp30) REVERT: H 67 ARG cc_start: 0.9331 (ttp-110) cc_final: 0.8856 (ttm110) REVERT: H 68 ASP cc_start: 0.9310 (m-30) cc_final: 0.8696 (p0) REVERT: H 73 THR cc_start: 0.9704 (m) cc_final: 0.9480 (p) REVERT: H 74 GLU cc_start: 0.7970 (tp30) cc_final: 0.7475 (tp30) REVERT: H 88 TYR cc_start: 0.9019 (m-10) cc_final: 0.8764 (m-10) REVERT: I 38 ASN cc_start: 0.9382 (m110) cc_final: 0.9133 (m110) REVERT: I 64 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8616 (tm-30) REVERT: I 84 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8781 (tp-100) REVERT: I 90 ASP cc_start: 0.8950 (t0) cc_final: 0.8472 (t0) REVERT: I 92 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7348 (mt-10) REVERT: I 104 GLN cc_start: 0.8823 (mp10) cc_final: 0.7933 (mp10) REVERT: J 65 ASP cc_start: 0.9259 (t0) cc_final: 0.8994 (t0) REVERT: J 96 ARG cc_start: 0.9144 (mtp180) cc_final: 0.8788 (ttm110) REVERT: J 102 GLU cc_start: 0.8714 (pm20) cc_final: 0.8334 (pm20) REVERT: J 103 LEU cc_start: 0.9546 (mt) cc_final: 0.9294 (mt) REVERT: K 73 GLU cc_start: 0.8226 (tt0) cc_final: 0.7664 (tt0) REVERT: K 77 ASP cc_start: 0.9354 (t70) cc_final: 0.9130 (t0) REVERT: K 84 PHE cc_start: 0.8725 (m-80) cc_final: 0.8415 (m-80) REVERT: K 94 GLU cc_start: 0.9078 (tp30) cc_final: 0.8511 (tp30) REVERT: K 99 TYR cc_start: 0.8574 (t80) cc_final: 0.8305 (t80) REVERT: K 105 GLU cc_start: 0.9377 (tt0) cc_final: 0.8962 (pp20) REVERT: K 110 CYS cc_start: 0.8872 (t) cc_final: 0.8671 (t) REVERT: K 117 VAL cc_start: 0.9346 (m) cc_final: 0.9079 (p) REVERT: K 125 GLN cc_start: 0.9117 (pt0) cc_final: 0.8515 (pp30) REVERT: L 22 LEU cc_start: 0.8342 (mm) cc_final: 0.7904 (mm) REVERT: L 25 ASN cc_start: 0.8486 (m110) cc_final: 0.7538 (m110) REVERT: L 67 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8185 (ttp80) REVERT: L 72 TYR cc_start: 0.9385 (m-10) cc_final: 0.9011 (m-10) REVERT: L 85 ASP cc_start: 0.9148 (m-30) cc_final: 0.8763 (m-30) REVERT: L 93 GLN cc_start: 0.9220 (tp40) cc_final: 0.8998 (tp40) REVERT: L 98 TYR cc_start: 0.8747 (m-10) cc_final: 0.8245 (m-80) REVERT: M 41 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8347 (mp0) REVERT: M 57 TYR cc_start: 0.9019 (t80) cc_final: 0.8279 (t80) REVERT: M 64 GLU cc_start: 0.9179 (pp20) cc_final: 0.8895 (pp20) REVERT: M 68 ASN cc_start: 0.8595 (m110) cc_final: 0.7913 (m110) REVERT: M 95 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8748 (ttmt) REVERT: M 99 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7999 (mmp80) REVERT: M 108 LEU cc_start: 0.9571 (pt) cc_final: 0.9230 (pt) REVERT: N 69 ARG cc_start: 0.9209 (ttm170) cc_final: 0.8857 (ttm110) REVERT: N 81 ASN cc_start: 0.9138 (t0) cc_final: 0.8825 (t0) REVERT: N 92 GLN cc_start: 0.9261 (tt0) cc_final: 0.8794 (tm-30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1455 time to fit residues: 79.1217 Evaluate side-chains 301 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 39 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN K 39 HIS K 68 GLN L 27 GLN M 104 GLN N 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.108742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068280 restraints weight = 91974.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070449 restraints weight = 45817.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071751 restraints weight = 29024.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072537 restraints weight = 21475.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.072978 restraints weight = 17829.726| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 20565 Z= 0.264 Angle : 0.710 10.056 29072 Z= 0.398 Chirality : 0.044 0.205 3279 Planarity : 0.006 0.073 2665 Dihedral : 29.566 177.975 5081 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % 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 are not related in a simple way. whole: -0.94 (0.19), residues: 1699 helix: 0.60 (0.20), residues: 584 sheet: -0.68 (0.27), residues: 353 loop : -1.54 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 92 TYR 0.030 0.002 TYR G 54 PHE 0.018 0.002 PHE G 67 TRP 0.024 0.002 TRP D 327 HIS 0.017 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00578 (20565) covalent geometry : angle 0.71033 (29072) hydrogen bonds : bond 0.08213 ( 1048) hydrogen bonds : angle 4.74268 ( 2646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.1321 (mmtt) cc_final: 0.0834 (mtmt) REVERT: A 213 PHE cc_start: 0.5012 (p90) cc_final: 0.4396 (p90) REVERT: C 3931 MET cc_start: -0.0454 (mtp) cc_final: -0.0922 (ttm) REVERT: D 336 MET cc_start: 0.4908 (tmm) cc_final: 0.3068 (mmt) REVERT: G 50 GLU cc_start: 0.9161 (tp30) cc_final: 0.8896 (tp30) REVERT: G 65 LEU cc_start: 0.9470 (mm) cc_final: 0.9208 (mm) REVERT: G 104 PHE cc_start: 0.9507 (m-80) cc_final: 0.9219 (m-80) REVERT: G 119 ILE cc_start: 0.8685 (pt) cc_final: 0.7323 (pt) REVERT: G 120 MET cc_start: 0.8415 (tpt) cc_final: 0.8061 (mmp) REVERT: G 130 ILE cc_start: 0.9566 (mm) cc_final: 0.9364 (tp) REVERT: H 27 GLN cc_start: 0.9003 (pp30) cc_final: 0.8746 (pp30) REVERT: H 44 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8786 (tppt) REVERT: H 63 GLU cc_start: 0.8965 (tp30) cc_final: 0.8667 (tp30) REVERT: H 67 ARG cc_start: 0.9365 (ttp-110) cc_final: 0.8917 (ttm110) REVERT: H 68 ASP cc_start: 0.9130 (m-30) cc_final: 0.8720 (p0) REVERT: H 75 HIS cc_start: 0.8852 (t-90) cc_final: 0.8529 (t-90) REVERT: I 38 ASN cc_start: 0.9319 (m110) cc_final: 0.9043 (m110) REVERT: I 57 TYR cc_start: 0.7850 (t80) cc_final: 0.6957 (t80) REVERT: I 61 GLU cc_start: 0.8867 (mp0) cc_final: 0.8159 (mp0) REVERT: I 64 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8626 (tm-30) REVERT: I 77 ARG cc_start: 0.8650 (mtm110) cc_final: 0.8123 (mtm180) REVERT: I 84 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8806 (tp-100) REVERT: I 90 ASP cc_start: 0.8904 (t0) cc_final: 0.8382 (t0) REVERT: I 92 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7179 (mt-10) REVERT: I 104 GLN cc_start: 0.8897 (mp10) cc_final: 0.8170 (mp10) REVERT: J 65 ASP cc_start: 0.9244 (t0) cc_final: 0.8957 (t0) REVERT: J 96 ARG cc_start: 0.9104 (mtp180) cc_final: 0.8772 (ttm110) REVERT: J 103 LEU cc_start: 0.9438 (mt) cc_final: 0.9101 (mt) REVERT: K 64 LYS cc_start: 0.9315 (mmtp) cc_final: 0.8998 (mmtm) REVERT: K 73 GLU cc_start: 0.8173 (tt0) cc_final: 0.7673 (tt0) REVERT: K 84 PHE cc_start: 0.8706 (m-80) cc_final: 0.8426 (m-80) REVERT: K 99 TYR cc_start: 0.8646 (t80) cc_final: 0.8283 (t80) REVERT: K 105 GLU cc_start: 0.9315 (tt0) cc_final: 0.8952 (pp20) REVERT: K 110 CYS cc_start: 0.8849 (t) cc_final: 0.8607 (t) REVERT: K 117 VAL cc_start: 0.9391 (m) cc_final: 0.9138 (p) REVERT: K 125 GLN cc_start: 0.9122 (pt0) cc_final: 0.8478 (pp30) REVERT: L 22 LEU cc_start: 0.8357 (mm) cc_final: 0.7896 (mm) REVERT: L 25 ASN cc_start: 0.8475 (m110) cc_final: 0.7488 (m110) REVERT: L 36 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8237 (mtm-85) REVERT: L 66 ILE cc_start: 0.9817 (mp) cc_final: 0.9478 (tt) REVERT: L 67 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8243 (ttp80) REVERT: L 72 TYR cc_start: 0.9349 (m-10) cc_final: 0.9010 (m-10) REVERT: L 75 HIS cc_start: 0.9195 (t-90) cc_final: 0.8815 (t70) REVERT: L 85 ASP cc_start: 0.9247 (m-30) cc_final: 0.8759 (m-30) REVERT: L 93 GLN cc_start: 0.9258 (tp40) cc_final: 0.9000 (tp40) REVERT: L 95 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.7498 (mmm-85) REVERT: L 98 TYR cc_start: 0.8711 (m-10) cc_final: 0.8110 (m-80) REVERT: M 41 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8368 (mp0) REVERT: M 57 TYR cc_start: 0.9039 (t80) cc_final: 0.8229 (t80) REVERT: M 64 GLU cc_start: 0.9204 (pp20) cc_final: 0.8942 (pp20) REVERT: M 68 ASN cc_start: 0.8708 (m110) cc_final: 0.8079 (m110) REVERT: M 95 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8841 (ttmt) REVERT: M 99 ARG cc_start: 0.8235 (mmt180) cc_final: 0.7953 (mmp80) REVERT: N 65 ASP cc_start: 0.8814 (t0) cc_final: 0.8321 (t0) REVERT: N 69 ARG cc_start: 0.9224 (ttm170) cc_final: 0.8611 (ttm110) REVERT: N 83 ARG cc_start: 0.9249 (tpp-160) cc_final: 0.8804 (tpp80) REVERT: N 92 GLN cc_start: 0.9300 (tt0) cc_final: 0.8598 (tm-30) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.1406 time to fit residues: 77.8643 Evaluate side-chains 300 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 93 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN J 60 ASN J 92 GLN J 106 HIS K 68 GLN M 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.109683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068930 restraints weight = 92542.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071172 restraints weight = 46376.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072509 restraints weight = 29301.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073304 restraints weight = 21839.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073760 restraints weight = 18279.548| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 20565 Z= 0.221 Angle : 0.688 10.391 29072 Z= 0.384 Chirality : 0.043 0.260 3279 Planarity : 0.006 0.091 2665 Dihedral : 29.498 178.303 5081 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.07 % Allowed : 1.72 % Favored : 98.22 % 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 are not related in a simple way. whole: -0.79 (0.19), residues: 1699 helix: 0.78 (0.20), residues: 588 sheet: -0.63 (0.27), residues: 359 loop : -1.50 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 92 TYR 0.030 0.002 TYR L 51 PHE 0.016 0.002 PHE G 67 TRP 0.027 0.002 TRP D 327 HIS 0.011 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00486 (20565) covalent geometry : angle 0.68764 (29072) hydrogen bonds : bond 0.07895 ( 1048) hydrogen bonds : angle 4.58783 ( 2646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.0981 (mm) cc_final: 0.0568 (pt) REVERT: A 80 LYS cc_start: 0.1303 (mmtt) cc_final: 0.0797 (mtmt) REVERT: A 213 PHE cc_start: 0.5006 (p90) cc_final: 0.4448 (p90) REVERT: C 3931 MET cc_start: -0.0380 (mtp) cc_final: -0.0879 (ttm) REVERT: D 336 MET cc_start: 0.4837 (tmm) cc_final: 0.3018 (mmt) REVERT: G 50 GLU cc_start: 0.9076 (tp30) cc_final: 0.8819 (tp30) REVERT: G 55 GLN cc_start: 0.8973 (mt0) cc_final: 0.8509 (mt0) REVERT: G 82 LEU cc_start: 0.8934 (mm) cc_final: 0.8697 (mm) REVERT: G 104 PHE cc_start: 0.9499 (m-80) cc_final: 0.9185 (m-80) REVERT: G 119 ILE cc_start: 0.8626 (pt) cc_final: 0.7300 (pt) REVERT: G 120 MET cc_start: 0.8309 (tpt) cc_final: 0.8014 (mmp) REVERT: H 27 GLN cc_start: 0.8959 (pp30) cc_final: 0.8703 (pp30) REVERT: H 67 ARG cc_start: 0.9284 (ttp-110) cc_final: 0.8881 (ttm110) REVERT: H 97 LEU cc_start: 0.9130 (tp) cc_final: 0.8922 (tp) REVERT: I 38 ASN cc_start: 0.9249 (m110) cc_final: 0.9014 (m110) REVERT: I 57 TYR cc_start: 0.7883 (t80) cc_final: 0.7130 (t80) REVERT: I 61 GLU cc_start: 0.8868 (mp0) cc_final: 0.8372 (mp0) REVERT: I 64 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8560 (tm-30) REVERT: I 79 ILE cc_start: 0.9625 (tp) cc_final: 0.9397 (tp) REVERT: I 84 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8814 (tp-100) REVERT: I 90 ASP cc_start: 0.8751 (t0) cc_final: 0.8261 (t0) REVERT: I 92 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7696 (mt-10) REVERT: I 100 VAL cc_start: 0.9659 (t) cc_final: 0.9179 (t) REVERT: I 104 GLN cc_start: 0.8860 (mp10) cc_final: 0.7990 (mp10) REVERT: J 96 ARG cc_start: 0.9108 (mtp180) cc_final: 0.8747 (ttm110) REVERT: J 103 LEU cc_start: 0.9393 (mt) cc_final: 0.8874 (mt) REVERT: K 73 GLU cc_start: 0.8227 (tt0) cc_final: 0.7726 (tt0) REVERT: K 77 ASP cc_start: 0.9368 (t70) cc_final: 0.9161 (t0) REVERT: K 84 PHE cc_start: 0.8781 (m-80) cc_final: 0.8565 (m-80) REVERT: K 90 MET cc_start: 0.9231 (mmp) cc_final: 0.8995 (mmt) REVERT: K 94 GLU cc_start: 0.9024 (tp30) cc_final: 0.8559 (tp30) REVERT: K 99 TYR cc_start: 0.8574 (t80) cc_final: 0.8367 (t80) REVERT: K 105 GLU cc_start: 0.9307 (tt0) cc_final: 0.8909 (pp20) REVERT: K 110 CYS cc_start: 0.8823 (t) cc_final: 0.8293 (t) REVERT: K 117 VAL cc_start: 0.9364 (m) cc_final: 0.9114 (p) REVERT: K 123 ASP cc_start: 0.7435 (t70) cc_final: 0.6200 (t70) REVERT: K 125 GLN cc_start: 0.9118 (pt0) cc_final: 0.8431 (pp30) REVERT: L 22 LEU cc_start: 0.8319 (mm) cc_final: 0.7852 (mm) REVERT: L 25 ASN cc_start: 0.8483 (m110) cc_final: 0.7600 (m110) REVERT: L 36 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8212 (mtm-85) REVERT: L 66 ILE cc_start: 0.9806 (mp) cc_final: 0.9399 (tt) REVERT: L 67 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8215 (ttp80) REVERT: L 72 TYR cc_start: 0.9275 (m-10) cc_final: 0.8904 (m-10) REVERT: L 85 ASP cc_start: 0.9157 (m-30) cc_final: 0.8719 (m-30) REVERT: L 93 GLN cc_start: 0.9223 (tp40) cc_final: 0.9001 (tp40) REVERT: M 23 LEU cc_start: 0.8858 (mt) cc_final: 0.8596 (mt) REVERT: M 41 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8307 (mp0) REVERT: M 56 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9170 (mt-10) REVERT: M 64 GLU cc_start: 0.9215 (pp20) cc_final: 0.8929 (pp20) REVERT: M 68 ASN cc_start: 0.8703 (m110) cc_final: 0.8067 (m110) REVERT: M 89 ASN cc_start: 0.9117 (m-40) cc_final: 0.8843 (m-40) REVERT: M 95 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8736 (ttmt) REVERT: M 99 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7944 (mmp80) REVERT: M 108 LEU cc_start: 0.9597 (pt) cc_final: 0.9295 (pt) REVERT: N 38 VAL cc_start: 0.9762 (t) cc_final: 0.9419 (t) REVERT: N 65 ASP cc_start: 0.8756 (t0) cc_final: 0.8297 (t0) REVERT: N 69 ARG cc_start: 0.9221 (ttm170) cc_final: 0.8615 (ttm110) REVERT: N 83 ARG cc_start: 0.9158 (tpp-160) cc_final: 0.8730 (tpp80) REVERT: N 92 GLN cc_start: 0.9251 (tt0) cc_final: 0.8617 (tm-30) outliers start: 1 outliers final: 1 residues processed: 352 average time/residue: 0.1308 time to fit residues: 71.7144 Evaluate side-chains 298 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 62 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 44 optimal weight: 50.0000 chunk 182 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 178 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN G 76 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS K 39 HIS K 68 GLN L 27 GLN M 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.109329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069084 restraints weight = 91708.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071323 restraints weight = 45376.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072643 restraints weight = 28545.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073430 restraints weight = 21055.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073901 restraints weight = 17432.559| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 20565 Z= 0.230 Angle : 0.695 10.815 29072 Z= 0.387 Chirality : 0.044 0.223 3279 Planarity : 0.006 0.070 2665 Dihedral : 29.440 178.107 5081 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.07 % Allowed : 1.10 % Favored : 98.83 % 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 are not related in a simple way. whole: -0.84 (0.19), residues: 1699 helix: 0.79 (0.20), residues: 577 sheet: -0.74 (0.27), residues: 376 loop : -1.49 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 20 TYR 0.027 0.002 TYR G 54 PHE 0.023 0.002 PHE D 394 TRP 0.031 0.002 TRP D 327 HIS 0.010 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00509 (20565) covalent geometry : angle 0.69481 (29072) hydrogen bonds : bond 0.08037 ( 1048) hydrogen bonds : angle 4.61586 ( 2646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.1016 (mm) cc_final: 0.0623 (pt) REVERT: A 80 LYS cc_start: 0.1061 (mmtt) cc_final: 0.0554 (mtmt) REVERT: A 213 PHE cc_start: 0.5021 (p90) cc_final: 0.4502 (p90) REVERT: C 3931 MET cc_start: -0.0192 (mtp) cc_final: -0.0691 (ttm) REVERT: D 336 MET cc_start: 0.4897 (tmm) cc_final: 0.3051 (mmt) REVERT: G 55 GLN cc_start: 0.8948 (mt0) cc_final: 0.8482 (mt0) REVERT: G 58 THR cc_start: 0.9517 (p) cc_final: 0.9311 (p) REVERT: G 65 LEU cc_start: 0.9461 (mm) cc_final: 0.8887 (tp) REVERT: G 104 PHE cc_start: 0.9520 (m-80) cc_final: 0.9265 (m-80) REVERT: G 108 ASN cc_start: 0.9401 (t0) cc_final: 0.9151 (t0) REVERT: G 119 ILE cc_start: 0.8644 (pt) cc_final: 0.7170 (pt) REVERT: G 120 MET cc_start: 0.8350 (tpt) cc_final: 0.8010 (mmp) REVERT: G 133 GLU cc_start: 0.7128 (mp0) cc_final: 0.6793 (mp0) REVERT: H 27 GLN cc_start: 0.8970 (pp30) cc_final: 0.8694 (pp30) REVERT: H 44 LYS cc_start: 0.9438 (tppt) cc_final: 0.9235 (tppt) REVERT: H 63 GLU cc_start: 0.8978 (tp30) cc_final: 0.8730 (tp30) REVERT: H 67 ARG cc_start: 0.9225 (ttp-110) cc_final: 0.8975 (ttm110) REVERT: H 98 TYR cc_start: 0.9155 (m-80) cc_final: 0.8747 (m-80) REVERT: I 38 ASN cc_start: 0.9259 (m110) cc_final: 0.8999 (m110) REVERT: I 64 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8619 (tm-30) REVERT: I 84 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8824 (tp-100) REVERT: I 90 ASP cc_start: 0.8839 (t0) cc_final: 0.8354 (t0) REVERT: I 92 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7393 (mt-10) REVERT: I 104 GLN cc_start: 0.8849 (mp10) cc_final: 0.8306 (mp10) REVERT: J 92 GLN cc_start: 0.9318 (pt0) cc_final: 0.8897 (pt0) REVERT: J 96 ARG cc_start: 0.9117 (mtp180) cc_final: 0.8762 (ttm110) REVERT: J 103 LEU cc_start: 0.9360 (mt) cc_final: 0.9116 (mt) REVERT: K 73 GLU cc_start: 0.8239 (tt0) cc_final: 0.7647 (tt0) REVERT: K 77 ASP cc_start: 0.9396 (t70) cc_final: 0.9186 (t0) REVERT: K 84 PHE cc_start: 0.8847 (m-80) cc_final: 0.8474 (m-80) REVERT: K 93 GLN cc_start: 0.8656 (pp30) cc_final: 0.8287 (tm-30) REVERT: K 105 GLU cc_start: 0.9328 (tt0) cc_final: 0.8942 (pp20) REVERT: K 110 CYS cc_start: 0.8854 (t) cc_final: 0.8621 (t) REVERT: K 117 VAL cc_start: 0.9368 (m) cc_final: 0.9133 (p) REVERT: K 125 GLN cc_start: 0.9117 (pt0) cc_final: 0.8480 (pp30) REVERT: L 22 LEU cc_start: 0.8285 (mm) cc_final: 0.7881 (mm) REVERT: L 25 ASN cc_start: 0.8407 (m110) cc_final: 0.7538 (m110) REVERT: L 67 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8256 (ttp80) REVERT: L 72 TYR cc_start: 0.9294 (m-10) cc_final: 0.8923 (m-10) REVERT: L 85 ASP cc_start: 0.9226 (m-30) cc_final: 0.8697 (m-30) REVERT: L 98 TYR cc_start: 0.8494 (m-80) cc_final: 0.7983 (m-80) REVERT: M 41 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8252 (mp0) REVERT: M 57 TYR cc_start: 0.9094 (t80) cc_final: 0.8401 (t80) REVERT: M 64 GLU cc_start: 0.9214 (pp20) cc_final: 0.8954 (pp20) REVERT: M 68 ASN cc_start: 0.8662 (m110) cc_final: 0.8048 (m110) REVERT: M 95 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8712 (ttmt) REVERT: M 99 ARG cc_start: 0.8170 (mmt180) cc_final: 0.7880 (mmp80) REVERT: M 108 LEU cc_start: 0.9588 (pt) cc_final: 0.9269 (pt) REVERT: N 56 MET cc_start: 0.8953 (tpp) cc_final: 0.8689 (tpp) REVERT: N 65 ASP cc_start: 0.8754 (t0) cc_final: 0.8448 (t0) REVERT: N 69 ARG cc_start: 0.9231 (ttm170) cc_final: 0.8753 (ttm110) REVERT: N 92 GLN cc_start: 0.9246 (tt0) cc_final: 0.8833 (tm-30) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 0.1268 time to fit residues: 69.3588 Evaluate side-chains 295 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 13 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN H 25 ASN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN M 104 GLN M 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.110543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070047 restraints weight = 90914.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072321 restraints weight = 45328.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073625 restraints weight = 28534.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074402 restraints weight = 21007.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074914 restraints weight = 17446.313| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 20565 Z= 0.201 Angle : 0.681 10.700 29072 Z= 0.377 Chirality : 0.043 0.250 3279 Planarity : 0.006 0.070 2665 Dihedral : 29.360 178.029 5081 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.25 % 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 are not related in a simple way. whole: -0.77 (0.20), residues: 1699 helix: 0.77 (0.20), residues: 587 sheet: -0.67 (0.27), residues: 377 loop : -1.44 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 20 TYR 0.025 0.002 TYR K 54 PHE 0.021 0.002 PHE K 67 TRP 0.028 0.002 TRP D 327 HIS 0.009 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00446 (20565) covalent geometry : angle 0.68073 (29072) hydrogen bonds : bond 0.07662 ( 1048) hydrogen bonds : angle 4.49772 ( 2646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.0822 (mm) cc_final: 0.0405 (pt) REVERT: A 80 LYS cc_start: 0.1292 (mmtt) cc_final: 0.0789 (mtmt) REVERT: A 213 PHE cc_start: 0.5115 (p90) cc_final: 0.4573 (p90) REVERT: B 81 LYS cc_start: 0.5972 (mmtp) cc_final: 0.5771 (mttt) REVERT: C 3931 MET cc_start: -0.0057 (mtp) cc_final: -0.0543 (ttm) REVERT: D 336 MET cc_start: 0.5022 (tmm) cc_final: 0.2961 (mmt) REVERT: G 50 GLU cc_start: 0.8999 (tp30) cc_final: 0.8617 (tp30) REVERT: G 51 ILE cc_start: 0.9313 (mt) cc_final: 0.9037 (mt) REVERT: G 55 GLN cc_start: 0.8934 (mt0) cc_final: 0.8441 (mt0) REVERT: G 58 THR cc_start: 0.9477 (p) cc_final: 0.9226 (p) REVERT: G 65 LEU cc_start: 0.9454 (mm) cc_final: 0.8884 (tp) REVERT: G 82 LEU cc_start: 0.8954 (mm) cc_final: 0.8738 (mm) REVERT: G 108 ASN cc_start: 0.9409 (t0) cc_final: 0.9140 (t0) REVERT: G 119 ILE cc_start: 0.8597 (pt) cc_final: 0.7215 (pt) REVERT: H 27 GLN cc_start: 0.8885 (pp30) cc_final: 0.8626 (pm20) REVERT: H 44 LYS cc_start: 0.9404 (tppt) cc_final: 0.9000 (tppt) REVERT: H 63 GLU cc_start: 0.8935 (tp30) cc_final: 0.8652 (tp30) REVERT: H 67 ARG cc_start: 0.9137 (ttp-110) cc_final: 0.8886 (ttm110) REVERT: H 98 TYR cc_start: 0.9088 (m-80) cc_final: 0.8866 (m-80) REVERT: I 38 ASN cc_start: 0.9222 (m110) cc_final: 0.8999 (m110) REVERT: I 64 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8553 (tm-30) REVERT: I 79 ILE cc_start: 0.9603 (tt) cc_final: 0.9324 (tp) REVERT: I 84 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8792 (tp-100) REVERT: I 90 ASP cc_start: 0.8731 (t0) cc_final: 0.8240 (t0) REVERT: I 104 GLN cc_start: 0.8890 (mp10) cc_final: 0.8324 (mp10) REVERT: J 92 GLN cc_start: 0.9241 (pt0) cc_final: 0.8748 (pt0) REVERT: J 96 ARG cc_start: 0.9108 (mtp180) cc_final: 0.8764 (ttm110) REVERT: K 73 GLU cc_start: 0.8282 (tt0) cc_final: 0.7705 (tt0) REVERT: K 77 ASP cc_start: 0.9381 (t70) cc_final: 0.9161 (t0) REVERT: K 84 PHE cc_start: 0.8887 (m-80) cc_final: 0.8573 (m-80) REVERT: K 93 GLN cc_start: 0.8616 (pp30) cc_final: 0.8262 (tm-30) REVERT: K 105 GLU cc_start: 0.9295 (tt0) cc_final: 0.9002 (pp20) REVERT: K 107 THR cc_start: 0.9516 (p) cc_final: 0.9207 (p) REVERT: K 117 VAL cc_start: 0.9370 (m) cc_final: 0.9085 (p) REVERT: L 22 LEU cc_start: 0.8246 (mm) cc_final: 0.7893 (mm) REVERT: L 25 ASN cc_start: 0.8451 (m110) cc_final: 0.7690 (m110) REVERT: L 45 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8644 (tpp80) REVERT: L 82 THR cc_start: 0.9431 (p) cc_final: 0.9105 (p) REVERT: M 57 TYR cc_start: 0.9038 (t80) cc_final: 0.8432 (t80) REVERT: M 64 GLU cc_start: 0.9208 (pp20) cc_final: 0.8942 (pp20) REVERT: M 68 ASN cc_start: 0.8671 (m110) cc_final: 0.8013 (m110) REVERT: M 89 ASN cc_start: 0.9076 (m-40) cc_final: 0.8784 (m-40) REVERT: M 99 ARG cc_start: 0.8138 (mmt180) cc_final: 0.7756 (mmp80) REVERT: M 108 LEU cc_start: 0.9585 (pt) cc_final: 0.9187 (pt) REVERT: N 40 LYS cc_start: 0.9446 (tttp) cc_final: 0.9195 (tptt) REVERT: N 56 MET cc_start: 0.8969 (tpp) cc_final: 0.8634 (tpp) REVERT: N 65 ASP cc_start: 0.8894 (t0) cc_final: 0.8618 (t0) REVERT: N 69 ARG cc_start: 0.9228 (ttm170) cc_final: 0.8812 (ttm110) REVERT: N 92 GLN cc_start: 0.9282 (tt0) cc_final: 0.8841 (tm-30) outliers start: 1 outliers final: 0 residues processed: 348 average time/residue: 0.1429 time to fit residues: 77.1081 Evaluate side-chains 290 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN J 106 HIS K 39 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN L 27 GLN M 104 GLN N 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.108455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068317 restraints weight = 92707.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070489 restraints weight = 46424.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071822 restraints weight = 29395.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072653 restraints weight = 21799.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073094 restraints weight = 18160.881| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 20565 Z= 0.256 Angle : 0.717 10.558 29072 Z= 0.399 Chirality : 0.044 0.245 3279 Planarity : 0.006 0.073 2665 Dihedral : 29.387 177.351 5081 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1699 helix: 0.63 (0.20), residues: 587 sheet: -0.68 (0.27), residues: 378 loop : -1.49 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 20 TYR 0.036 0.002 TYR K 54 PHE 0.043 0.002 PHE K 67 TRP 0.026 0.002 TRP D 327 HIS 0.011 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00569 (20565) covalent geometry : angle 0.71745 (29072) hydrogen bonds : bond 0.08452 ( 1048) hydrogen bonds : angle 4.72394 ( 2646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.0717 (mm) cc_final: 0.0319 (pt) REVERT: A 80 LYS cc_start: 0.1182 (mmtt) cc_final: 0.0697 (mtmt) REVERT: A 213 PHE cc_start: 0.5117 (p90) cc_final: 0.4544 (p90) REVERT: B 314 ASN cc_start: 0.6056 (m-40) cc_final: 0.5724 (t0) REVERT: C 3931 MET cc_start: -0.0047 (mtp) cc_final: -0.0665 (ttp) REVERT: G 50 GLU cc_start: 0.9185 (tp30) cc_final: 0.8775 (tp30) REVERT: G 55 GLN cc_start: 0.8956 (mt0) cc_final: 0.8429 (mt0) REVERT: G 58 THR cc_start: 0.9564 (p) cc_final: 0.9218 (p) REVERT: G 65 LEU cc_start: 0.9493 (mm) cc_final: 0.8928 (tp) REVERT: G 108 ASN cc_start: 0.9402 (t0) cc_final: 0.9131 (t0) REVERT: G 119 ILE cc_start: 0.8482 (pt) cc_final: 0.7800 (pt) REVERT: G 120 MET cc_start: 0.8305 (mmp) cc_final: 0.7763 (mmm) REVERT: H 27 GLN cc_start: 0.8899 (pp30) cc_final: 0.8672 (pm20) REVERT: H 44 LYS cc_start: 0.9476 (tppt) cc_final: 0.9275 (tppt) REVERT: H 63 GLU cc_start: 0.9082 (tp30) cc_final: 0.8796 (tp30) REVERT: H 67 ARG cc_start: 0.9244 (ttp-110) cc_final: 0.8969 (ttm110) REVERT: H 98 TYR cc_start: 0.9174 (m-80) cc_final: 0.8813 (m-80) REVERT: I 61 GLU cc_start: 0.9015 (mp0) cc_final: 0.8635 (mp0) REVERT: I 64 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8723 (tm-30) REVERT: I 84 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8834 (tp-100) REVERT: I 104 GLN cc_start: 0.8890 (mp10) cc_final: 0.8322 (mp10) REVERT: J 81 ASN cc_start: 0.9392 (t0) cc_final: 0.9052 (t0) REVERT: J 83 ARG cc_start: 0.8872 (mtp180) cc_final: 0.8590 (mtp180) REVERT: J 92 GLN cc_start: 0.9292 (pt0) cc_final: 0.8839 (pt0) REVERT: J 96 ARG cc_start: 0.9189 (mtp180) cc_final: 0.8747 (ttm110) REVERT: J 103 LEU cc_start: 0.9304 (mt) cc_final: 0.9088 (mp) REVERT: K 73 GLU cc_start: 0.8295 (tt0) cc_final: 0.7627 (tt0) REVERT: K 77 ASP cc_start: 0.9440 (t70) cc_final: 0.9216 (t0) REVERT: K 84 PHE cc_start: 0.8903 (m-80) cc_final: 0.8290 (m-80) REVERT: K 93 GLN cc_start: 0.8573 (pp30) cc_final: 0.8273 (tm-30) REVERT: K 105 GLU cc_start: 0.9437 (tt0) cc_final: 0.9008 (pp20) REVERT: L 22 LEU cc_start: 0.8242 (mm) cc_final: 0.7937 (mm) REVERT: L 25 ASN cc_start: 0.8421 (m110) cc_final: 0.7504 (m110) REVERT: L 88 TYR cc_start: 0.8702 (m-10) cc_final: 0.8309 (m-10) REVERT: M 57 TYR cc_start: 0.9085 (t80) cc_final: 0.8569 (t80) REVERT: M 64 GLU cc_start: 0.9266 (pp20) cc_final: 0.8999 (pp20) REVERT: M 68 ASN cc_start: 0.8652 (m110) cc_final: 0.8035 (m110) REVERT: M 99 ARG cc_start: 0.8236 (mmt180) cc_final: 0.7705 (mmp80) REVERT: M 108 LEU cc_start: 0.9570 (pt) cc_final: 0.9202 (pt) REVERT: N 53 SER cc_start: 0.8823 (p) cc_final: 0.8512 (m) REVERT: N 56 MET cc_start: 0.9053 (tpp) cc_final: 0.8817 (tpp) REVERT: N 65 ASP cc_start: 0.8969 (t0) cc_final: 0.8700 (t0) REVERT: N 69 ARG cc_start: 0.9291 (ttm170) cc_final: 0.8835 (ttm110) REVERT: N 83 ARG cc_start: 0.8958 (tpp80) cc_final: 0.8537 (tpp80) REVERT: N 85 THR cc_start: 0.8925 (p) cc_final: 0.8572 (p) REVERT: N 92 GLN cc_start: 0.9322 (tt0) cc_final: 0.8850 (tm-30) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.1388 time to fit residues: 74.2910 Evaluate side-chains 295 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 11 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN J 106 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS M 104 GLN N 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.107040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067243 restraints weight = 93535.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069281 restraints weight = 47161.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070549 restraints weight = 30108.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071346 restraints weight = 22383.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071756 restraints weight = 18709.947| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 20565 Z= 0.287 Angle : 0.738 10.723 29072 Z= 0.412 Chirality : 0.045 0.247 3279 Planarity : 0.006 0.074 2665 Dihedral : 29.511 176.617 5081 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1699 helix: 0.47 (0.20), residues: 585 sheet: -0.59 (0.27), residues: 377 loop : -1.59 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 20 TYR 0.050 0.003 TYR H 88 PHE 0.020 0.002 PHE I 25 TRP 0.025 0.002 TRP D 327 HIS 0.011 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00632 (20565) covalent geometry : angle 0.73836 (29072) hydrogen bonds : bond 0.08711 ( 1048) hydrogen bonds : angle 4.86320 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5145.82 seconds wall clock time: 89 minutes 9.25 seconds (5349.25 seconds total)