Starting phenix.real_space_refine on Mon Oct 13 07:59:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5m_21543/10_2025/6w5m_21543.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5m_21543/10_2025/6w5m_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_21543/10_2025/6w5m_21543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5m_21543/10_2025/6w5m_21543.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5m_21543/10_2025/6w5m_21543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5m_21543/10_2025/6w5m_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/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: 5.07, per 1000 atoms: 0.26 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: 1.77 Conformation dependent library (CDL) restraints added in 678.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 3.05 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: 4.86 Time building geometry restraints manager: 2.40 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- 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 aren 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 : 0.619 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: 0.0821 (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: 0.9191 (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 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: 0.1950 time to fit residues: 147.3699 Evaluate side-chains 355 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 348 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 N 106 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.112353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.070666 restraints weight = 90973.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.072815 restraints weight = 46108.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073973 restraints weight = 29668.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074746 restraints weight = 22365.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.075217 restraints weight = 18928.668| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 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 = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 20565 Z= 0.284 Angle : 0.735 7.067 29072 Z= 0.412 Chirality : 0.045 0.216 3279 Planarity : 0.006 0.063 2665 Dihedral : 29.656 177.237 5081 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.21 % Allowed : 5.22 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.19), residues: 1699 helix: 0.10 (0.20), residues: 591 sheet: -1.27 (0.25), residues: 375 loop : -1.77 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 32 TYR 0.026 0.002 TYR M 39 PHE 0.030 0.003 PHE K 67 TRP 0.023 0.002 TRP D 505 HIS 0.007 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00612 (20565) covalent geometry : angle 0.73533 (29072) hydrogen bonds : bond 0.08623 ( 1048) hydrogen bonds : angle 5.02317 ( 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 421 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 418 time to evaluate : 0.477 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: symmetry clash REVERT: A 18 ASP cc_start: 0.1383 (t0) cc_final: 0.0954 (m-30) REVERT: A 80 LYS cc_start: 0.0832 (mmtt) cc_final: 0.0422 (mtmt) REVERT: A 134 MET cc_start: -0.1051 (mtm) cc_final: -0.1316 (mtm) REVERT: A 213 PHE cc_start: 0.5144 (p90) cc_final: 0.4215 (p90) REVERT: C 3883 TYR cc_start: 0.4887 (m-80) cc_final: 0.4605 (m-80) REVERT: C 3884 MET cc_start: 0.2206 (ttp) cc_final: 0.1524 (tmm) REVERT: C 3931 MET cc_start: -0.0532 (mtp) cc_final: -0.1125 (ttt) REVERT: D 336 MET cc_start: 0.3992 (tmm) cc_final: 0.3422 (mmt) REVERT: D 337 PRO cc_start: 0.2472 (Cg_exo) cc_final: 0.1828 (Cg_endo) REVERT: D 518 TYR cc_start: -0.2050 (t80) cc_final: -0.2315 (m-10) REVERT: G 55 GLN cc_start: 0.8893 (mt0) cc_final: 0.8469 (mt0) REVERT: G 61 LEU cc_start: 0.8414 (mm) cc_final: 0.8099 (mm) REVERT: G 97 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 120 MET cc_start: 0.8410 (tpt) cc_final: 0.8081 (mmm) REVERT: H 27 GLN cc_start: 0.8840 (pp30) cc_final: 0.8359 (pp30) REVERT: H 64 ASN cc_start: 0.9230 (m-40) cc_final: 0.8643 (m-40) REVERT: H 65 VAL cc_start: 0.9784 (m) cc_final: 0.9325 (p) REVERT: H 67 ARG cc_start: 0.9287 (ttp-110) cc_final: 0.8815 (ttp80) REVERT: H 68 ASP cc_start: 0.9220 (m-30) cc_final: 0.8822 (p0) REVERT: H 75 HIS cc_start: 0.8245 (t-90) cc_final: 0.7912 (t-90) REVERT: H 84 MET cc_start: 0.8960 (mmm) cc_final: 0.8730 (mmm) REVERT: H 88 TYR cc_start: 0.8877 (m-10) cc_final: 0.8513 (m-10) REVERT: I 38 ASN cc_start: 0.9214 (m110) cc_final: 0.8954 (m-40) REVERT: I 50 TYR cc_start: 0.9288 (t80) cc_final: 0.9077 (t80) REVERT: I 64 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8475 (tm-30) REVERT: I 90 ASP cc_start: 0.8985 (t0) cc_final: 0.8696 (t0) REVERT: I 92 GLU cc_start: 0.8175 (mt-10) cc_final: 0.6502 (mt-10) REVERT: I 99 ARG cc_start: 0.9005 (ptp90) cc_final: 0.8769 (mtm-85) REVERT: I 102 ILE cc_start: 0.9527 (tp) cc_final: 0.9190 (tp) REVERT: J 96 ARG cc_start: 0.8990 (mtp180) cc_final: 0.8676 (ttm110) REVERT: J 97 LEU cc_start: 0.9491 (tt) cc_final: 0.9193 (tt) REVERT: J 103 LEU cc_start: 0.9423 (mt) cc_final: 0.8649 (mt) REVERT: J 106 HIS cc_start: 0.8555 (m90) cc_final: 0.7956 (m170) REVERT: K 73 GLU cc_start: 0.8495 (tt0) cc_final: 0.7978 (tt0) REVERT: K 77 ASP cc_start: 0.9262 (t0) cc_final: 0.9058 (t70) REVERT: K 80 THR cc_start: 0.8229 (p) cc_final: 0.7448 (p) REVERT: K 81 ASP cc_start: 0.8462 (m-30) cc_final: 0.8072 (m-30) REVERT: K 84 PHE cc_start: 0.8601 (m-80) cc_final: 0.8199 (m-80) REVERT: K 85 GLN cc_start: 0.8808 (mp-120) cc_final: 0.8328 (mm110) REVERT: K 90 MET cc_start: 0.9148 (mmm) cc_final: 0.8948 (mmm) REVERT: K 93 GLN cc_start: 0.8908 (pp30) cc_final: 0.7612 (pp30) REVERT: K 94 GLU cc_start: 0.8970 (tp30) cc_final: 0.8574 (tp30) REVERT: K 120 MET cc_start: 0.8761 (tpp) cc_final: 0.8554 (mmm) REVERT: K 122 LYS cc_start: 0.8844 (pttp) cc_final: 0.8388 (pttt) REVERT: L 25 ASN cc_start: 0.8618 (m110) cc_final: 0.7699 (m110) REVERT: L 37 LEU cc_start: 0.9392 (mt) cc_final: 0.8971 (mt) REVERT: L 66 ILE cc_start: 0.9712 (OUTLIER) cc_final: 0.9354 (tt) REVERT: L 85 ASP cc_start: 0.9028 (m-30) cc_final: 0.8798 (m-30) REVERT: M 68 ASN cc_start: 0.7932 (m-40) cc_final: 0.7613 (m110) REVERT: M 87 VAL cc_start: 0.9139 (t) cc_final: 0.8932 (t) REVERT: M 88 ARG cc_start: 0.9313 (mmt180) cc_final: 0.9071 (mmp80) REVERT: M 100 VAL cc_start: 0.9508 (t) cc_final: 0.9206 (t) REVERT: M 108 LEU cc_start: 0.9329 (pt) cc_final: 0.9090 (pt) REVERT: N 48 ASP cc_start: 0.8472 (p0) cc_final: 0.8186 (t0) REVERT: N 58 ILE cc_start: 0.9283 (mt) cc_final: 0.9072 (mt) REVERT: N 68 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8202 (mm-30) REVERT: N 76 ARG cc_start: 0.9155 (ttm-80) cc_final: 0.8880 (ttm-80) REVERT: N 81 ASN cc_start: 0.8735 (t0) cc_final: 0.8291 (t0) REVERT: N 92 GLN cc_start: 0.9069 (tt0) cc_final: 0.8531 (tm-30) outliers start: 3 outliers final: 0 residues processed: 419 average time/residue: 0.1707 time to fit residues: 103.5929 Evaluate side-chains 325 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 2.9990 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.111332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070319 restraints weight = 90220.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.072310 restraints weight = 44592.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.073633 restraints weight = 28244.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074440 restraints weight = 21088.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074831 restraints weight = 17668.245| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 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 = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 20565 Z= 0.254 Angle : 0.701 9.493 29072 Z= 0.391 Chirality : 0.044 0.258 3279 Planarity : 0.006 0.095 2665 Dihedral : 29.580 177.686 5081 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.19), residues: 1699 helix: 0.55 (0.20), residues: 599 sheet: -1.14 (0.26), residues: 374 loop : -1.50 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 29 TYR 0.022 0.002 TYR M 39 PHE 0.029 0.002 PHE G 67 TRP 0.022 0.002 TRP D 327 HIS 0.010 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00556 (20565) covalent geometry : angle 0.70067 (29072) hydrogen bonds : bond 0.08260 ( 1048) hydrogen bonds : angle 4.69611 ( 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 393 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.639 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: A 80 LYS cc_start: 0.1006 (mmtt) cc_final: 0.0526 (mtmt) REVERT: A 213 PHE cc_start: 0.5011 (p90) cc_final: 0.4244 (p90) REVERT: D 336 MET cc_start: 0.4010 (tmm) cc_final: 0.3204 (mmt) REVERT: G 55 GLN cc_start: 0.8879 (mt0) cc_final: 0.8465 (mt0) REVERT: G 65 LEU cc_start: 0.9446 (mm) cc_final: 0.9194 (mm) REVERT: G 119 ILE cc_start: 0.8484 (pt) cc_final: 0.7415 (pt) REVERT: G 120 MET cc_start: 0.8269 (tpt) cc_final: 0.8017 (mmp) REVERT: G 130 ILE cc_start: 0.9475 (mm) cc_final: 0.9104 (mm) REVERT: H 27 GLN cc_start: 0.8896 (pp30) cc_final: 0.8642 (pp30) REVERT: H 44 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8704 (tppt) REVERT: H 74 GLU cc_start: 0.8024 (tp30) cc_final: 0.7776 (tp30) REVERT: H 75 HIS cc_start: 0.8308 (t-90) cc_final: 0.7866 (t-170) REVERT: H 84 MET cc_start: 0.8709 (mmm) cc_final: 0.8490 (mmm) REVERT: H 88 TYR cc_start: 0.8939 (m-10) cc_final: 0.8572 (m-10) REVERT: I 17 ARG cc_start: 0.9334 (mtm180) cc_final: 0.8679 (ttm110) REVERT: I 38 ASN cc_start: 0.9267 (m110) cc_final: 0.8966 (m110) REVERT: I 64 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8553 (tm-30) REVERT: I 90 ASP cc_start: 0.9044 (t0) cc_final: 0.8553 (t0) REVERT: I 91 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8599 (tm-30) REVERT: I 92 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7085 (mt-10) REVERT: I 99 ARG cc_start: 0.8862 (ptp90) cc_final: 0.8374 (ttm110) REVERT: I 104 GLN cc_start: 0.8815 (mp10) cc_final: 0.8143 (mp10) REVERT: J 37 TYR cc_start: 0.8876 (m-80) cc_final: 0.8658 (m-80) REVERT: J 57 SER cc_start: 0.9574 (m) cc_final: 0.9369 (p) REVERT: J 96 ARG cc_start: 0.9082 (mtp180) cc_final: 0.8850 (ttm110) REVERT: J 103 LEU cc_start: 0.9424 (mt) cc_final: 0.9085 (mt) REVERT: K 73 GLU cc_start: 0.8352 (tt0) cc_final: 0.7642 (tt0) REVERT: K 80 THR cc_start: 0.8452 (p) cc_final: 0.7693 (p) REVERT: K 81 ASP cc_start: 0.8552 (m-30) cc_final: 0.8225 (m-30) REVERT: K 84 PHE cc_start: 0.8656 (m-80) cc_final: 0.8373 (m-80) REVERT: K 85 GLN cc_start: 0.9086 (mp10) cc_final: 0.8761 (mm-40) REVERT: K 90 MET cc_start: 0.9189 (mmm) cc_final: 0.8944 (mmm) REVERT: K 105 GLU cc_start: 0.9182 (tt0) cc_final: 0.8856 (pp20) REVERT: K 117 VAL cc_start: 0.9232 (m) cc_final: 0.8914 (p) REVERT: K 120 MET cc_start: 0.8318 (mmt) cc_final: 0.8049 (mmt) REVERT: L 25 ASN cc_start: 0.8532 (m110) cc_final: 0.7757 (m110) REVERT: L 39 ARG cc_start: 0.9173 (mmt180) cc_final: 0.8827 (mmm160) REVERT: L 45 ARG cc_start: 0.9006 (tpp80) cc_final: 0.8680 (tpp80) REVERT: L 63 GLU cc_start: 0.8754 (tp30) cc_final: 0.8467 (tm-30) REVERT: L 75 HIS cc_start: 0.9118 (t70) cc_final: 0.8885 (t-170) REVERT: L 85 ASP cc_start: 0.9115 (m-30) cc_final: 0.8882 (m-30) REVERT: M 57 TYR cc_start: 0.9352 (t80) cc_final: 0.8231 (t80) REVERT: M 64 GLU cc_start: 0.9087 (pp20) cc_final: 0.8559 (pp20) REVERT: M 65 LEU cc_start: 0.9566 (mt) cc_final: 0.9285 (mt) REVERT: M 68 ASN cc_start: 0.8677 (m-40) cc_final: 0.8001 (m110) REVERT: M 87 VAL cc_start: 0.9266 (t) cc_final: 0.8912 (t) REVERT: M 88 ARG cc_start: 0.9348 (mmt180) cc_final: 0.8962 (mmp80) REVERT: M 108 LEU cc_start: 0.9573 (pt) cc_final: 0.9351 (pt) REVERT: N 30 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7153 (mtt180) REVERT: N 59 MET cc_start: 0.9182 (mmp) cc_final: 0.8956 (mmm) REVERT: N 68 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8141 (mm-30) REVERT: N 81 ASN cc_start: 0.8863 (t0) cc_final: 0.8376 (t0) REVERT: N 92 GLN cc_start: 0.9168 (tt0) cc_final: 0.8611 (tm-30) REVERT: N 93 THR cc_start: 0.9295 (p) cc_final: 0.8978 (p) outliers start: 1 outliers final: 0 residues processed: 392 average time/residue: 0.1655 time to fit residues: 96.2120 Evaluate side-chains 319 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 8.9990 chunk 190 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 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 60 ASN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.110036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069691 restraints weight = 90970.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071880 restraints weight = 44879.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073232 restraints weight = 27922.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074073 restraints weight = 20468.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.074524 restraints weight = 16910.336| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 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 = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 20565 Z= 0.249 Angle : 0.687 9.833 29072 Z= 0.386 Chirality : 0.044 0.231 3279 Planarity : 0.005 0.059 2665 Dihedral : 29.526 178.235 5081 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.19), residues: 1699 helix: 0.67 (0.20), residues: 600 sheet: -0.88 (0.26), residues: 357 loop : -1.49 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 76 TYR 0.026 0.002 TYR H 98 PHE 0.022 0.002 PHE G 67 TRP 0.024 0.002 TRP D 505 HIS 0.010 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00545 (20565) covalent geometry : angle 0.68734 (29072) hydrogen bonds : bond 0.08209 ( 1048) hydrogen bonds : angle 4.65452 ( 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 382 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.649 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: A 61 ILE cc_start: 0.0925 (mm) cc_final: 0.0377 (pt) REVERT: A 80 LYS cc_start: 0.1161 (mmtt) cc_final: 0.0654 (mtmt) REVERT: A 213 PHE cc_start: 0.4897 (p90) cc_final: 0.4283 (p90) REVERT: C 3931 MET cc_start: -0.0618 (mtt) cc_final: -0.1880 (ttt) REVERT: D 336 MET cc_start: 0.4035 (tmm) cc_final: 0.3020 (mmt) REVERT: G 55 GLN cc_start: 0.8882 (mt0) cc_final: 0.8550 (mt0) REVERT: G 65 LEU cc_start: 0.9452 (mm) cc_final: 0.9218 (mm) REVERT: G 119 ILE cc_start: 0.8566 (pt) cc_final: 0.7382 (pt) REVERT: G 120 MET cc_start: 0.8393 (tpt) cc_final: 0.7987 (mmp) REVERT: H 27 GLN cc_start: 0.8940 (pp30) cc_final: 0.8651 (pp30) REVERT: H 29 ILE cc_start: 0.9466 (mm) cc_final: 0.9241 (pt) REVERT: H 44 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8299 (mmtm) REVERT: H 73 THR cc_start: 0.9714 (m) cc_final: 0.9448 (p) REVERT: H 74 GLU cc_start: 0.8012 (tp30) cc_final: 0.7681 (tp30) REVERT: H 88 TYR cc_start: 0.9019 (m-10) cc_final: 0.8735 (m-10) REVERT: I 25 PHE cc_start: 0.9078 (m-10) cc_final: 0.8820 (m-80) REVERT: I 38 ASN cc_start: 0.9362 (m110) cc_final: 0.9065 (m110) REVERT: I 64 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8598 (tm-30) REVERT: I 84 GLN cc_start: 0.9415 (tp-100) cc_final: 0.8820 (tp-100) REVERT: I 90 ASP cc_start: 0.9016 (t0) cc_final: 0.8536 (t0) REVERT: I 104 GLN cc_start: 0.8799 (mp10) cc_final: 0.8187 (mp10) REVERT: J 37 TYR cc_start: 0.8912 (m-80) cc_final: 0.8594 (m-80) REVERT: J 96 ARG cc_start: 0.9100 (mtp180) cc_final: 0.8676 (ttm110) REVERT: K 51 ILE cc_start: 0.9338 (mt) cc_final: 0.9123 (mt) REVERT: K 73 GLU cc_start: 0.8259 (tt0) cc_final: 0.7644 (tt0) REVERT: K 84 PHE cc_start: 0.8684 (m-80) cc_final: 0.8305 (m-80) REVERT: K 85 GLN cc_start: 0.9230 (mp10) cc_final: 0.8941 (mm110) REVERT: K 90 MET cc_start: 0.9329 (mmm) cc_final: 0.9061 (mmm) REVERT: K 97 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8650 (mt-10) REVERT: K 99 TYR cc_start: 0.8565 (t80) cc_final: 0.8325 (t80) REVERT: K 105 GLU cc_start: 0.9298 (tt0) cc_final: 0.8931 (pp20) REVERT: K 117 VAL cc_start: 0.9347 (m) cc_final: 0.9080 (p) REVERT: L 22 LEU cc_start: 0.8285 (mm) cc_final: 0.7849 (mm) REVERT: L 25 ASN cc_start: 0.8549 (m110) cc_final: 0.7841 (m110) REVERT: L 39 ARG cc_start: 0.9129 (mmt180) cc_final: 0.8720 (mmm160) REVERT: L 63 GLU cc_start: 0.8657 (tp30) cc_final: 0.8421 (tp30) REVERT: L 67 ARG cc_start: 0.8879 (ttp80) cc_final: 0.8308 (ttp80) REVERT: L 84 MET cc_start: 0.8838 (mpp) cc_final: 0.8413 (mpp) REVERT: L 88 TYR cc_start: 0.8737 (m-10) cc_final: 0.8278 (m-80) REVERT: M 41 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8310 (mp0) REVERT: M 57 TYR cc_start: 0.9329 (t80) cc_final: 0.8182 (t80) REVERT: M 64 GLU cc_start: 0.9093 (pp20) cc_final: 0.8788 (pp20) REVERT: M 68 ASN cc_start: 0.8604 (m-40) cc_final: 0.8032 (m110) REVERT: M 88 ARG cc_start: 0.9293 (mmt180) cc_final: 0.8879 (mmt90) REVERT: M 91 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8252 (tm-30) REVERT: M 108 LEU cc_start: 0.9569 (pt) cc_final: 0.9348 (pt) REVERT: N 30 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7815 (mtt180) REVERT: N 92 GLN cc_start: 0.9272 (tt0) cc_final: 0.8644 (tm-30) outliers start: 2 outliers final: 0 residues processed: 381 average time/residue: 0.1566 time to fit residues: 90.2876 Evaluate side-chains 303 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 7.9990 chunk 153 optimal weight: 5.9990 chunk 134 optimal weight: 0.0980 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 50.0000 chunk 183 optimal weight: 4.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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** D 375 HIS G 76 GLN H 64 ASN J 46 HIS J 106 HIS K 39 HIS K 68 GLN M 104 GLN ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.108257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067616 restraints weight = 92584.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069704 restraints weight = 46705.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071047 restraints weight = 29600.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.071896 restraints weight = 21990.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072323 restraints weight = 18330.232| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 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 = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 20565 Z= 0.278 Angle : 0.723 11.226 29072 Z= 0.405 Chirality : 0.045 0.231 3279 Planarity : 0.006 0.099 2665 Dihedral : 29.548 178.090 5081 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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 aren not related in a simple way. whole: -0.95 (0.19), residues: 1699 helix: 0.59 (0.20), residues: 588 sheet: -0.77 (0.26), residues: 363 loop : -1.50 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 81 TYR 0.019 0.002 TYR H 98 PHE 0.020 0.002 PHE G 67 TRP 0.027 0.002 TRP D 327 HIS 0.012 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00607 (20565) covalent geometry : angle 0.72259 (29072) hydrogen bonds : bond 0.08590 ( 1048) hydrogen bonds : angle 4.77416 ( 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 356 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.676 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: 0.0725 (mm) cc_final: 0.0213 (pt) REVERT: A 80 LYS cc_start: 0.1029 (mmtt) cc_final: 0.0471 (mtmt) REVERT: A 213 PHE cc_start: 0.4972 (p90) cc_final: 0.4362 (p90) REVERT: C 3931 MET cc_start: -0.0859 (mtt) cc_final: -0.1920 (ttt) REVERT: D 336 MET cc_start: 0.4723 (tmm) cc_final: 0.3086 (mmt) REVERT: G 55 GLN cc_start: 0.8949 (mt0) cc_final: 0.8381 (mt0) REVERT: G 65 LEU cc_start: 0.9507 (mm) cc_final: 0.9268 (mm) REVERT: G 104 PHE cc_start: 0.9582 (m-80) cc_final: 0.9336 (m-80) REVERT: G 119 ILE cc_start: 0.8580 (pt) cc_final: 0.7295 (pt) REVERT: G 120 MET cc_start: 0.8459 (tpt) cc_final: 0.8094 (mmp) REVERT: G 130 ILE cc_start: 0.9588 (mm) cc_final: 0.9351 (tp) REVERT: G 133 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7486 (mp0) REVERT: H 27 GLN cc_start: 0.9019 (pp30) cc_final: 0.8726 (pp30) REVERT: H 29 ILE cc_start: 0.9501 (mm) cc_final: 0.9136 (pt) REVERT: H 88 TYR cc_start: 0.9031 (m-10) cc_final: 0.8829 (m-80) REVERT: I 38 ASN cc_start: 0.9306 (m110) cc_final: 0.9048 (m110) REVERT: I 50 TYR cc_start: 0.9357 (t80) cc_final: 0.9024 (t80) REVERT: I 64 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8601 (tm-30) REVERT: I 84 GLN cc_start: 0.9316 (tp-100) cc_final: 0.8855 (tp-100) REVERT: I 90 ASP cc_start: 0.8898 (t0) cc_final: 0.8330 (t0) REVERT: I 104 GLN cc_start: 0.8908 (mp10) cc_final: 0.8207 (mp10) REVERT: J 34 TYR cc_start: 0.9490 (m-80) cc_final: 0.9242 (m-10) REVERT: J 37 TYR cc_start: 0.8916 (m-80) cc_final: 0.8618 (m-80) REVERT: J 96 ARG cc_start: 0.9140 (mtp180) cc_final: 0.8837 (ttm110) REVERT: J 102 GLU cc_start: 0.9214 (pt0) cc_final: 0.8677 (mp0) REVERT: J 103 LEU cc_start: 0.9519 (mp) cc_final: 0.8566 (mm) REVERT: J 106 HIS cc_start: 0.8507 (m90) cc_final: 0.8285 (m-70) REVERT: K 51 ILE cc_start: 0.9375 (mt) cc_final: 0.9137 (mt) REVERT: K 73 GLU cc_start: 0.8223 (tt0) cc_final: 0.7658 (tt0) REVERT: K 77 ASP cc_start: 0.9371 (t70) cc_final: 0.9086 (t0) REVERT: K 84 PHE cc_start: 0.8680 (m-80) cc_final: 0.8327 (m-80) REVERT: K 99 TYR cc_start: 0.8593 (t80) cc_final: 0.8331 (t80) REVERT: K 105 GLU cc_start: 0.9340 (tt0) cc_final: 0.8919 (pp20) REVERT: K 117 VAL cc_start: 0.9381 (m) cc_final: 0.9092 (p) REVERT: L 22 LEU cc_start: 0.8358 (mm) cc_final: 0.7934 (mm) REVERT: L 25 ASN cc_start: 0.8471 (m110) cc_final: 0.7602 (m110) REVERT: L 39 ARG cc_start: 0.9170 (mmt180) cc_final: 0.8364 (mmt180) REVERT: L 45 ARG cc_start: 0.9231 (tpp80) cc_final: 0.8892 (tpp80) REVERT: L 63 GLU cc_start: 0.8590 (tp30) cc_final: 0.7933 (tm-30) REVERT: L 67 ARG cc_start: 0.8782 (ttp80) cc_final: 0.8288 (ttp80) REVERT: L 72 TYR cc_start: 0.9311 (m-10) cc_final: 0.8992 (m-10) REVERT: L 85 ASP cc_start: 0.9212 (m-30) cc_final: 0.8837 (m-30) REVERT: L 88 TYR cc_start: 0.8804 (m-10) cc_final: 0.8450 (m-10) REVERT: L 93 GLN cc_start: 0.9230 (tp40) cc_final: 0.8968 (tp40) REVERT: L 98 TYR cc_start: 0.8868 (m-10) cc_final: 0.8452 (m-80) REVERT: M 41 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8287 (mp0) REVERT: M 57 TYR cc_start: 0.9207 (t80) cc_final: 0.8369 (t80) REVERT: M 64 GLU cc_start: 0.9123 (pp20) cc_final: 0.8768 (pp20) REVERT: M 68 ASN cc_start: 0.8719 (m-40) cc_final: 0.8009 (m110) REVERT: M 87 VAL cc_start: 0.9296 (t) cc_final: 0.8987 (t) REVERT: M 91 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8311 (tm-30) REVERT: M 108 LEU cc_start: 0.9576 (pt) cc_final: 0.9249 (pt) REVERT: N 38 VAL cc_start: 0.9774 (t) cc_final: 0.9339 (t) REVERT: N 81 ASN cc_start: 0.9092 (t0) cc_final: 0.8739 (t0) REVERT: N 92 GLN cc_start: 0.9240 (tt0) cc_final: 0.8608 (tm-30) REVERT: N 93 THR cc_start: 0.9295 (p) cc_final: 0.9034 (p) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1465 time to fit residues: 79.9875 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 : 0.617 ------------------------------------------------------------------------------- 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: 20.0000 chunk 143 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** 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 N 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.110415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069984 restraints weight = 90177.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072121 restraints weight = 44646.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073464 restraints weight = 28023.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074250 restraints weight = 20761.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074713 restraints weight = 17308.952| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 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 = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 20565 Z= 0.213 Angle : 0.678 9.734 29072 Z= 0.381 Chirality : 0.043 0.252 3279 Planarity : 0.005 0.066 2665 Dihedral : 29.475 178.312 5081 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 1699 helix: 0.95 (0.20), residues: 578 sheet: -0.88 (0.27), residues: 358 loop : -1.39 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 20 TYR 0.017 0.002 TYR I 50 PHE 0.019 0.002 PHE K 104 TRP 0.025 0.002 TRP D 327 HIS 0.019 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00465 (20565) covalent geometry : angle 0.67764 (29072) hydrogen bonds : bond 0.07838 ( 1048) hydrogen bonds : angle 4.54310 ( 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 359 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 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: A 61 ILE cc_start: 0.1240 (mm) cc_final: 0.0879 (pt) REVERT: A 80 LYS cc_start: 0.1191 (mmtt) cc_final: 0.0678 (mtmt) REVERT: A 213 PHE cc_start: 0.4918 (p90) cc_final: 0.4336 (p90) REVERT: C 3931 MET cc_start: -0.0947 (mtt) cc_final: -0.1819 (ttt) REVERT: D 336 MET cc_start: 0.4781 (tmm) cc_final: 0.2998 (mmt) REVERT: G 55 GLN cc_start: 0.8925 (mt0) cc_final: 0.8724 (mt0) REVERT: G 108 ASN cc_start: 0.9321 (t0) cc_final: 0.9083 (t0) REVERT: G 119 ILE cc_start: 0.8609 (pt) cc_final: 0.7285 (pt) REVERT: G 120 MET cc_start: 0.8332 (tpt) cc_final: 0.8002 (mmp) REVERT: G 124 ILE cc_start: 0.9547 (pt) cc_final: 0.9319 (pt) REVERT: G 130 ILE cc_start: 0.9584 (mm) cc_final: 0.9355 (tp) REVERT: G 133 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7432 (mp0) REVERT: H 27 GLN cc_start: 0.8975 (pp30) cc_final: 0.8646 (pp30) REVERT: H 29 ILE cc_start: 0.9518 (mm) cc_final: 0.9164 (pt) REVERT: H 44 LYS cc_start: 0.9441 (tppt) cc_final: 0.9235 (tppt) REVERT: H 97 LEU cc_start: 0.9064 (tp) cc_final: 0.8831 (tp) REVERT: I 38 ASN cc_start: 0.9242 (m110) cc_final: 0.9034 (m110) REVERT: I 57 TYR cc_start: 0.7946 (t80) cc_final: 0.7053 (t80) REVERT: I 61 GLU cc_start: 0.8825 (mp0) cc_final: 0.8162 (mp0) REVERT: I 64 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8594 (tm-30) REVERT: I 79 ILE cc_start: 0.9650 (tp) cc_final: 0.9432 (tp) REVERT: I 84 GLN cc_start: 0.9301 (tp-100) cc_final: 0.8888 (tp-100) REVERT: I 90 ASP cc_start: 0.8930 (t0) cc_final: 0.8399 (t0) REVERT: I 100 VAL cc_start: 0.9654 (t) cc_final: 0.9267 (t) REVERT: I 104 GLN cc_start: 0.8869 (mp10) cc_final: 0.8348 (mp10) REVERT: J 96 ARG cc_start: 0.9100 (mtp180) cc_final: 0.8739 (ttm110) REVERT: J 106 HIS cc_start: 0.8425 (m90) cc_final: 0.8039 (m170) REVERT: K 64 LYS cc_start: 0.9303 (mmtp) cc_final: 0.8890 (mmtm) REVERT: K 73 GLU cc_start: 0.8179 (tt0) cc_final: 0.7671 (tt0) REVERT: K 77 ASP cc_start: 0.9339 (t70) cc_final: 0.9084 (t0) REVERT: K 84 PHE cc_start: 0.8840 (m-80) cc_final: 0.8428 (m-80) REVERT: K 97 GLU cc_start: 0.9030 (mt-10) cc_final: 0.7797 (mm-30) REVERT: K 99 TYR cc_start: 0.8562 (t80) cc_final: 0.8327 (t80) REVERT: K 105 GLU cc_start: 0.9290 (tt0) cc_final: 0.8970 (pp20) REVERT: K 110 CYS cc_start: 0.8915 (t) cc_final: 0.8713 (t) REVERT: K 117 VAL cc_start: 0.9411 (m) cc_final: 0.9176 (p) REVERT: L 22 LEU cc_start: 0.8353 (mm) cc_final: 0.7937 (mm) REVERT: L 25 ASN cc_start: 0.8475 (m110) cc_final: 0.7552 (m110) REVERT: L 39 ARG cc_start: 0.9340 (mmt180) cc_final: 0.9031 (mmm-85) REVERT: L 63 GLU cc_start: 0.8533 (tp30) cc_final: 0.7821 (tm-30) REVERT: L 66 ILE cc_start: 0.9802 (mp) cc_final: 0.9466 (tt) REVERT: L 67 ARG cc_start: 0.8748 (ttp80) cc_final: 0.8213 (ttp80) REVERT: L 72 TYR cc_start: 0.9272 (m-10) cc_final: 0.9021 (m-10) REVERT: L 85 ASP cc_start: 0.9332 (m-30) cc_final: 0.8773 (m-30) REVERT: L 88 TYR cc_start: 0.8675 (m-10) cc_final: 0.8382 (m-80) REVERT: M 57 TYR cc_start: 0.9172 (t80) cc_final: 0.8434 (t80) REVERT: M 64 GLU cc_start: 0.9075 (pp20) cc_final: 0.8758 (pp20) REVERT: M 68 ASN cc_start: 0.8725 (m-40) cc_final: 0.8027 (m110) REVERT: M 87 VAL cc_start: 0.9308 (t) cc_final: 0.9066 (t) REVERT: M 91 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8359 (tm-30) REVERT: M 92 GLU cc_start: 0.8945 (tt0) cc_final: 0.8609 (tt0) REVERT: M 94 ASN cc_start: 0.9461 (t0) cc_final: 0.9196 (t0) REVERT: N 92 GLN cc_start: 0.9240 (tt0) cc_final: 0.8503 (tm-30) REVERT: N 93 THR cc_start: 0.9340 (p) cc_final: 0.9096 (p) REVERT: N 96 ARG cc_start: 0.8887 (mtp-110) cc_final: 0.8450 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1414 time to fit residues: 79.6562 Evaluate side-chains 306 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 88 ASN ** 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 J 60 ASN K 68 GLN M 104 GLN N 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.111049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070432 restraints weight = 90957.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072677 restraints weight = 45045.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.074020 restraints weight = 28324.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.074871 restraints weight = 20945.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.075392 restraints weight = 17423.103| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20565 Z= 0.189 Angle : 0.666 11.299 29072 Z= 0.372 Chirality : 0.043 0.280 3279 Planarity : 0.005 0.065 2665 Dihedral : 29.323 178.699 5081 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.07 % Allowed : 1.17 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.20), residues: 1699 helix: 0.89 (0.20), residues: 593 sheet: -0.74 (0.27), residues: 357 loop : -1.42 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 92 TYR 0.024 0.002 TYR H 88 PHE 0.016 0.002 PHE M 25 TRP 0.029 0.002 TRP D 327 HIS 0.018 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00417 (20565) covalent geometry : angle 0.66568 (29072) hydrogen bonds : bond 0.07700 ( 1048) hydrogen bonds : angle 4.44999 ( 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 355 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.781 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: A 61 ILE cc_start: 0.1167 (mm) cc_final: 0.0784 (pt) REVERT: A 80 LYS cc_start: 0.1332 (mmtt) cc_final: 0.0785 (mtmt) REVERT: A 213 PHE cc_start: 0.5013 (p90) cc_final: 0.4527 (p90) REVERT: C 3931 MET cc_start: -0.0920 (mtt) cc_final: -0.1799 (ttt) REVERT: D 336 MET cc_start: 0.4922 (tmm) cc_final: 0.2952 (mmt) REVERT: G 48 LEU cc_start: 0.9726 (tt) cc_final: 0.9434 (pp) REVERT: G 50 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8782 (tp30) REVERT: G 55 GLN cc_start: 0.8897 (mt0) cc_final: 0.8388 (mt0) REVERT: G 108 ASN cc_start: 0.9346 (t0) cc_final: 0.9086 (t0) REVERT: G 119 ILE cc_start: 0.8603 (pt) cc_final: 0.7236 (pt) REVERT: G 120 MET cc_start: 0.8239 (tpt) cc_final: 0.7939 (mmp) REVERT: G 130 ILE cc_start: 0.9584 (mm) cc_final: 0.9348 (tp) REVERT: G 133 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7469 (mp0) REVERT: H 27 GLN cc_start: 0.8956 (pp30) cc_final: 0.8633 (pp30) REVERT: H 29 ILE cc_start: 0.9490 (mm) cc_final: 0.9133 (pt) REVERT: H 44 LYS cc_start: 0.9514 (tppt) cc_final: 0.9306 (tppt) REVERT: H 97 LEU cc_start: 0.9129 (tp) cc_final: 0.8895 (tp) REVERT: I 25 PHE cc_start: 0.9124 (m-10) cc_final: 0.8886 (m-80) REVERT: I 38 ASN cc_start: 0.9213 (m110) cc_final: 0.8989 (m110) REVERT: I 64 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8596 (tm-30) REVERT: I 84 GLN cc_start: 0.9352 (tp-100) cc_final: 0.8935 (tp-100) REVERT: I 90 ASP cc_start: 0.8727 (t0) cc_final: 0.8282 (t0) REVERT: I 104 GLN cc_start: 0.8855 (mp10) cc_final: 0.8343 (mp10) REVERT: J 96 ARG cc_start: 0.9086 (mtp180) cc_final: 0.8727 (ttm110) REVERT: K 51 ILE cc_start: 0.9364 (mt) cc_final: 0.8863 (mt) REVERT: K 73 GLU cc_start: 0.8218 (tt0) cc_final: 0.7704 (tt0) REVERT: K 77 ASP cc_start: 0.9378 (t70) cc_final: 0.9108 (t0) REVERT: K 84 PHE cc_start: 0.8807 (m-80) cc_final: 0.8489 (m-80) REVERT: K 93 GLN cc_start: 0.8615 (pp30) cc_final: 0.8124 (pp30) REVERT: K 94 GLU cc_start: 0.8922 (tp30) cc_final: 0.8677 (tp30) REVERT: K 105 GLU cc_start: 0.9324 (tt0) cc_final: 0.8986 (pp20) REVERT: K 107 THR cc_start: 0.9522 (p) cc_final: 0.9201 (p) REVERT: K 117 VAL cc_start: 0.9441 (m) cc_final: 0.9187 (p) REVERT: L 22 LEU cc_start: 0.8236 (mm) cc_final: 0.7854 (mm) REVERT: L 25 ASN cc_start: 0.8403 (m110) cc_final: 0.7563 (m110) REVERT: L 39 ARG cc_start: 0.9319 (mmt180) cc_final: 0.8989 (mmm160) REVERT: L 43 VAL cc_start: 0.9505 (p) cc_final: 0.8992 (p) REVERT: L 44 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8436 (mmmt) REVERT: L 45 ARG cc_start: 0.9140 (tpp80) cc_final: 0.8792 (tpp80) REVERT: L 51 TYR cc_start: 0.8359 (m-80) cc_final: 0.8115 (m-80) REVERT: L 63 GLU cc_start: 0.8494 (tp30) cc_final: 0.7785 (tm-30) REVERT: L 66 ILE cc_start: 0.9811 (mp) cc_final: 0.9411 (tt) REVERT: L 67 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8336 (ttp80) REVERT: L 72 TYR cc_start: 0.9221 (m-10) cc_final: 0.8859 (m-10) REVERT: L 85 ASP cc_start: 0.9355 (m-30) cc_final: 0.8663 (m-30) REVERT: L 88 TYR cc_start: 0.8553 (m-10) cc_final: 0.8348 (m-80) REVERT: M 57 TYR cc_start: 0.9127 (t80) cc_final: 0.8390 (t80) REVERT: M 64 GLU cc_start: 0.9105 (pp20) cc_final: 0.8755 (pp20) REVERT: M 72 ASP cc_start: 0.8628 (m-30) cc_final: 0.8112 (t70) REVERT: M 87 VAL cc_start: 0.9323 (t) cc_final: 0.9098 (t) REVERT: M 94 ASN cc_start: 0.9478 (t0) cc_final: 0.9264 (t0) REVERT: M 108 LEU cc_start: 0.9612 (pt) cc_final: 0.9258 (pt) REVERT: N 39 TYR cc_start: 0.7417 (t80) cc_final: 0.7117 (t80) REVERT: N 43 LYS cc_start: 0.9494 (mmmt) cc_final: 0.9080 (mmmt) REVERT: N 81 ASN cc_start: 0.8985 (t160) cc_final: 0.8625 (t0) REVERT: N 92 GLN cc_start: 0.9232 (tt0) cc_final: 0.8663 (tm-30) REVERT: N 93 THR cc_start: 0.9357 (p) cc_final: 0.9065 (p) outliers start: 1 outliers final: 0 residues processed: 355 average time/residue: 0.1412 time to fit residues: 78.2144 Evaluate side-chains 303 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 3.9990 chunk 119 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 178 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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** A 250 ASN ** 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 106 HIS K 39 HIS K 68 GLN L 27 GLN M 104 GLN N 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.108361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068087 restraints weight = 92427.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070260 restraints weight = 46088.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071584 restraints weight = 29275.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072398 restraints weight = 21728.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072908 restraints weight = 18126.970| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 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 = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 20565 Z= 0.265 Angle : 0.712 11.406 29072 Z= 0.398 Chirality : 0.044 0.236 3279 Planarity : 0.006 0.069 2665 Dihedral : 29.354 177.775 5081 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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 aren not related in a simple way. whole: -0.85 (0.19), residues: 1699 helix: 0.71 (0.20), residues: 581 sheet: -0.73 (0.27), residues: 376 loop : -1.47 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 20 TYR 0.018 0.002 TYR N 37 PHE 0.018 0.002 PHE K 67 TRP 0.029 0.002 TRP D 327 HIS 0.017 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00587 (20565) covalent geometry : angle 0.71210 (29072) hydrogen bonds : bond 0.08499 ( 1048) hydrogen bonds : angle 4.73260 ( 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 339 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.652 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: 0.1171 (mm) cc_final: 0.0746 (pt) REVERT: A 80 LYS cc_start: 0.0856 (mmtt) cc_final: 0.0347 (mtmt) REVERT: A 213 PHE cc_start: 0.5046 (p90) cc_final: 0.4483 (p90) REVERT: C 3931 MET cc_start: -0.1183 (mtt) cc_final: -0.2033 (ttt) REVERT: D 336 MET cc_start: 0.4639 (tmm) cc_final: 0.2833 (mmt) REVERT: G 51 ILE cc_start: 0.9308 (mt) cc_final: 0.9043 (mt) REVERT: G 55 GLN cc_start: 0.8801 (mt0) cc_final: 0.8321 (mt0) REVERT: G 58 THR cc_start: 0.9537 (p) cc_final: 0.9216 (p) REVERT: G 65 LEU cc_start: 0.9503 (mm) cc_final: 0.9172 (mm) REVERT: G 82 LEU cc_start: 0.8954 (mm) cc_final: 0.8745 (mm) REVERT: G 119 ILE cc_start: 0.8665 (pt) cc_final: 0.7181 (pt) REVERT: G 120 MET cc_start: 0.8343 (tpt) cc_final: 0.8038 (mmp) REVERT: G 125 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8988 (tp40) REVERT: G 130 ILE cc_start: 0.9616 (mm) cc_final: 0.9297 (tp) REVERT: H 27 GLN cc_start: 0.8982 (pp30) cc_final: 0.8695 (pp30) REVERT: H 44 LYS cc_start: 0.9606 (tppt) cc_final: 0.9311 (tppt) REVERT: H 97 LEU cc_start: 0.9120 (tp) cc_final: 0.8914 (tp) REVERT: I 25 PHE cc_start: 0.9236 (m-10) cc_final: 0.8919 (m-10) REVERT: I 64 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8577 (tm-30) REVERT: I 84 GLN cc_start: 0.9362 (tp-100) cc_final: 0.8817 (tp-100) REVERT: I 90 ASP cc_start: 0.8882 (t0) cc_final: 0.8309 (t0) REVERT: J 96 ARG cc_start: 0.9178 (mtp180) cc_final: 0.8817 (ttm110) REVERT: J 102 GLU cc_start: 0.8523 (pp20) cc_final: 0.8214 (pp20) REVERT: J 103 LEU cc_start: 0.8935 (mp) cc_final: 0.8553 (mp) REVERT: J 105 LYS cc_start: 0.8826 (ptmm) cc_final: 0.8214 (mttt) REVERT: J 106 HIS cc_start: 0.8389 (m-70) cc_final: 0.7945 (m-70) REVERT: K 50 GLU cc_start: 0.8812 (pp20) cc_final: 0.8263 (pp20) REVERT: K 51 ILE cc_start: 0.9009 (mt) cc_final: 0.8516 (mm) REVERT: K 73 GLU cc_start: 0.8188 (tt0) cc_final: 0.7631 (tt0) REVERT: K 77 ASP cc_start: 0.9383 (t70) cc_final: 0.9161 (t0) REVERT: K 84 PHE cc_start: 0.8841 (m-80) cc_final: 0.8291 (m-80) REVERT: K 93 GLN cc_start: 0.8868 (pp30) cc_final: 0.8405 (pp30) REVERT: K 97 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8493 (mt-10) REVERT: K 99 TYR cc_start: 0.8579 (t80) cc_final: 0.8348 (t80) REVERT: K 105 GLU cc_start: 0.9378 (tt0) cc_final: 0.8973 (pp20) REVERT: K 117 VAL cc_start: 0.9417 (m) cc_final: 0.9167 (p) REVERT: L 22 LEU cc_start: 0.8310 (mm) cc_final: 0.7906 (mm) REVERT: L 25 ASN cc_start: 0.8452 (m110) cc_final: 0.7503 (m110) REVERT: L 39 ARG cc_start: 0.9403 (mmt180) cc_final: 0.8960 (mmm160) REVERT: L 63 GLU cc_start: 0.8528 (tp30) cc_final: 0.8259 (tp30) REVERT: L 66 ILE cc_start: 0.9814 (mp) cc_final: 0.9372 (tt) REVERT: L 67 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8253 (ttp80) REVERT: L 72 TYR cc_start: 0.9188 (m-10) cc_final: 0.8772 (m-10) REVERT: L 85 ASP cc_start: 0.9103 (m-30) cc_final: 0.8462 (m-30) REVERT: M 57 TYR cc_start: 0.9204 (t80) cc_final: 0.8454 (t80) REVERT: M 64 GLU cc_start: 0.9172 (pp20) cc_final: 0.8891 (pp20) REVERT: M 68 ASN cc_start: 0.8711 (m110) cc_final: 0.8074 (m110) REVERT: M 87 VAL cc_start: 0.9322 (t) cc_final: 0.9102 (t) REVERT: M 94 ASN cc_start: 0.9508 (t0) cc_final: 0.9256 (t0) REVERT: M 99 ARG cc_start: 0.8364 (mmt180) cc_final: 0.7940 (mmp80) REVERT: M 108 LEU cc_start: 0.9630 (pt) cc_final: 0.9250 (pt) REVERT: N 39 TYR cc_start: 0.7541 (t80) cc_final: 0.7084 (t80) REVERT: N 73 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8854 (mm-30) REVERT: N 81 ASN cc_start: 0.9020 (t160) cc_final: 0.8693 (t0) REVERT: N 92 GLN cc_start: 0.9199 (tt0) cc_final: 0.8624 (tm-30) REVERT: N 93 THR cc_start: 0.9400 (p) cc_final: 0.9054 (p) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.1385 time to fit residues: 74.1599 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 : 0.609 ------------------------------------------------------------------------------- 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: 9.9990 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 K 68 GLN ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.106425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066664 restraints weight = 91807.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068776 restraints weight = 45834.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070062 restraints weight = 29070.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070874 restraints weight = 21664.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071341 restraints weight = 18080.327| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 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 = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.7191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 20565 Z= 0.307 Angle : 0.755 10.790 29072 Z= 0.421 Chirality : 0.046 0.263 3279 Planarity : 0.006 0.073 2665 Dihedral : 29.485 177.117 5081 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1699 helix: 0.40 (0.20), residues: 587 sheet: -0.59 (0.27), residues: 363 loop : -1.63 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 131 TYR 0.018 0.002 TYR M 39 PHE 0.019 0.002 PHE G 67 TRP 0.025 0.002 TRP D 327 HIS 0.016 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00674 (20565) covalent geometry : angle 0.75526 (29072) hydrogen bonds : bond 0.08861 ( 1048) hydrogen bonds : angle 4.91212 ( 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 337 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.641 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: 0.1093 (mm) cc_final: 0.0626 (pt) REVERT: A 80 LYS cc_start: 0.1044 (mmtt) cc_final: 0.0510 (mtmt) REVERT: A 213 PHE cc_start: 0.5152 (p90) cc_final: 0.4724 (p90) REVERT: A 279 TRP cc_start: 0.1109 (m-90) cc_final: 0.0808 (m-90) REVERT: B 314 ASN cc_start: 0.6343 (m-40) cc_final: 0.5977 (t0) REVERT: C 3931 MET cc_start: -0.1050 (mtt) cc_final: -0.1780 (ttm) REVERT: D 327 TRP cc_start: 0.7552 (p-90) cc_final: 0.7342 (p-90) REVERT: G 51 ILE cc_start: 0.9429 (mt) cc_final: 0.9137 (mt) REVERT: G 55 GLN cc_start: 0.8847 (mt0) cc_final: 0.8337 (mt0) REVERT: G 65 LEU cc_start: 0.9489 (mm) cc_final: 0.9217 (mm) REVERT: G 104 PHE cc_start: 0.9536 (m-80) cc_final: 0.9122 (m-80) REVERT: G 119 ILE cc_start: 0.8535 (pt) cc_final: 0.7069 (pt) REVERT: G 120 MET cc_start: 0.8418 (tpt) cc_final: 0.8027 (mmm) REVERT: G 125 GLN cc_start: 0.9241 (mm-40) cc_final: 0.9031 (tp40) REVERT: H 44 LYS cc_start: 0.9624 (tppt) cc_final: 0.9249 (tppt) REVERT: H 63 GLU cc_start: 0.8973 (tp30) cc_final: 0.8200 (tp30) REVERT: I 25 PHE cc_start: 0.9217 (m-10) cc_final: 0.8888 (m-10) REVERT: I 61 GLU cc_start: 0.8856 (mp0) cc_final: 0.8322 (mp0) REVERT: I 64 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8663 (tm-30) REVERT: I 79 ILE cc_start: 0.9645 (tt) cc_final: 0.9355 (tp) REVERT: I 84 GLN cc_start: 0.9359 (tp-100) cc_final: 0.8927 (tp-100) REVERT: I 90 ASP cc_start: 0.8885 (t0) cc_final: 0.8357 (t0) REVERT: I 104 GLN cc_start: 0.8715 (mp10) cc_final: 0.8222 (mp10) REVERT: J 58 ILE cc_start: 0.9613 (mm) cc_final: 0.9342 (mm) REVERT: J 96 ARG cc_start: 0.9192 (mtp180) cc_final: 0.8861 (ttm110) REVERT: J 102 GLU cc_start: 0.8658 (pp20) cc_final: 0.8337 (pp20) REVERT: J 103 LEU cc_start: 0.8986 (mp) cc_final: 0.8660 (mp) REVERT: J 105 LYS cc_start: 0.8916 (ptmm) cc_final: 0.8342 (mttt) REVERT: K 73 GLU cc_start: 0.8128 (tt0) cc_final: 0.7532 (tt0) REVERT: K 77 ASP cc_start: 0.9402 (t70) cc_final: 0.9187 (t0) REVERT: K 84 PHE cc_start: 0.8771 (m-80) cc_final: 0.8211 (m-80) REVERT: K 93 GLN cc_start: 0.8881 (pp30) cc_final: 0.8458 (pp30) REVERT: K 97 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8586 (mt-10) REVERT: K 105 GLU cc_start: 0.9361 (tt0) cc_final: 0.8957 (pp20) REVERT: K 117 VAL cc_start: 0.9405 (m) cc_final: 0.9149 (p) REVERT: K 125 GLN cc_start: 0.8717 (pm20) cc_final: 0.8371 (pm20) REVERT: L 22 LEU cc_start: 0.8292 (mm) cc_final: 0.7938 (mm) REVERT: L 25 ASN cc_start: 0.8465 (m110) cc_final: 0.7371 (m110) REVERT: L 39 ARG cc_start: 0.9359 (mmt180) cc_final: 0.8896 (mmt180) REVERT: L 66 ILE cc_start: 0.9814 (mp) cc_final: 0.9447 (tt) REVERT: L 72 TYR cc_start: 0.9251 (m-10) cc_final: 0.8819 (m-10) REVERT: L 85 ASP cc_start: 0.9099 (m-30) cc_final: 0.8503 (m-30) REVERT: M 57 TYR cc_start: 0.9224 (t80) cc_final: 0.8486 (t80) REVERT: M 94 ASN cc_start: 0.9582 (t0) cc_final: 0.9305 (t0) REVERT: M 99 ARG cc_start: 0.8270 (mmt180) cc_final: 0.7904 (mmp80) REVERT: M 108 LEU cc_start: 0.9613 (pt) cc_final: 0.9237 (pt) REVERT: N 39 TYR cc_start: 0.7645 (t80) cc_final: 0.7394 (t80) REVERT: N 65 ASP cc_start: 0.8831 (t70) cc_final: 0.8601 (t0) REVERT: N 73 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8954 (mm-30) REVERT: N 81 ASN cc_start: 0.9070 (t160) cc_final: 0.8717 (t0) REVERT: N 92 GLN cc_start: 0.9221 (tt0) cc_final: 0.8837 (tm-30) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1430 time to fit residues: 75.7464 Evaluate side-chains 294 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 7.9990 chunk 65 optimal weight: 0.0040 chunk 117 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 2.1196 ------------------------------------------------------------------------------- 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 K 39 HIS K 68 GLN L 27 GLN N 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.109439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.069086 restraints weight = 91359.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071337 restraints weight = 45501.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072669 restraints weight = 28395.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073490 restraints weight = 21027.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073911 restraints weight = 17568.507| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- 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: 8 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20565 Z= 0.209 Angle : 0.705 12.292 29072 Z= 0.391 Chirality : 0.044 0.271 3279 Planarity : 0.006 0.086 2665 Dihedral : 29.370 177.521 5081 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.20), residues: 1699 helix: 0.56 (0.20), residues: 597 sheet: -0.68 (0.27), residues: 368 loop : -1.56 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 96 TYR 0.022 0.002 TYR H 88 PHE 0.021 0.002 PHE K 104 TRP 0.025 0.002 TRP D 327 HIS 0.015 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00464 (20565) covalent geometry : angle 0.70515 (29072) hydrogen bonds : bond 0.07893 ( 1048) hydrogen bonds : angle 4.64218 ( 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 337 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 0.618 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: A 61 ILE cc_start: 0.0896 (mm) cc_final: 0.0545 (pt) REVERT: A 80 LYS cc_start: 0.1250 (mmtt) cc_final: 0.0716 (mtmt) REVERT: A 213 PHE cc_start: 0.5126 (p90) cc_final: 0.4560 (p90) REVERT: A 279 TRP cc_start: 0.1184 (m-90) cc_final: 0.0896 (m-90) REVERT: B 314 ASN cc_start: 0.6353 (m-40) cc_final: 0.5886 (t0) REVERT: C 3931 MET cc_start: -0.1006 (mtt) cc_final: -0.1667 (ttm) REVERT: D 336 MET cc_start: 0.4264 (ptm) cc_final: 0.2602 (mtt) REVERT: G 51 ILE cc_start: 0.9263 (mt) cc_final: 0.8928 (mt) REVERT: G 55 GLN cc_start: 0.8899 (mt0) cc_final: 0.8383 (mt0) REVERT: G 58 THR cc_start: 0.9555 (p) cc_final: 0.9272 (p) REVERT: G 65 LEU cc_start: 0.9474 (mm) cc_final: 0.8928 (tp) REVERT: G 82 LEU cc_start: 0.8948 (mm) cc_final: 0.8746 (mm) REVERT: G 119 ILE cc_start: 0.8431 (pt) cc_final: 0.6995 (pt) REVERT: G 120 MET cc_start: 0.8315 (tpt) cc_final: 0.8029 (mmp) REVERT: G 130 ILE cc_start: 0.9610 (mm) cc_final: 0.9402 (tp) REVERT: H 44 LYS cc_start: 0.9584 (tppt) cc_final: 0.9274 (tppt) REVERT: I 25 PHE cc_start: 0.9245 (m-10) cc_final: 0.8881 (m-80) REVERT: I 38 ASN cc_start: 0.9284 (m110) cc_final: 0.9080 (m110) REVERT: I 50 TYR cc_start: 0.9072 (t80) cc_final: 0.8791 (t80) REVERT: I 61 GLU cc_start: 0.8780 (mp0) cc_final: 0.8320 (mp0) REVERT: I 64 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8683 (tm-30) REVERT: I 84 GLN cc_start: 0.9433 (tp-100) cc_final: 0.8999 (tp-100) REVERT: I 90 ASP cc_start: 0.8771 (t0) cc_final: 0.8110 (t0) REVERT: J 81 ASN cc_start: 0.9360 (t0) cc_final: 0.8939 (t0) REVERT: J 83 ARG cc_start: 0.8835 (mtp180) cc_final: 0.8631 (mtp180) REVERT: J 96 ARG cc_start: 0.9171 (mtp180) cc_final: 0.8775 (ttm110) REVERT: J 105 LYS cc_start: 0.8884 (ptmm) cc_final: 0.8223 (mttt) REVERT: J 106 HIS cc_start: 0.8506 (m-70) cc_final: 0.8109 (m-70) REVERT: K 50 GLU cc_start: 0.8857 (pp20) cc_final: 0.8341 (pp20) REVERT: K 51 ILE cc_start: 0.8849 (mt) cc_final: 0.8134 (mt) REVERT: K 64 LYS cc_start: 0.9148 (tppt) cc_final: 0.8847 (mmmm) REVERT: K 73 GLU cc_start: 0.8223 (tt0) cc_final: 0.7631 (tt0) REVERT: K 77 ASP cc_start: 0.9447 (t70) cc_final: 0.9227 (t0) REVERT: K 84 PHE cc_start: 0.8752 (m-80) cc_final: 0.8307 (m-80) REVERT: K 93 GLN cc_start: 0.8681 (pp30) cc_final: 0.7656 (pp30) REVERT: K 97 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8204 (mt-10) REVERT: K 105 GLU cc_start: 0.9404 (tt0) cc_final: 0.8948 (pp20) REVERT: K 117 VAL cc_start: 0.9381 (m) cc_final: 0.9113 (p) REVERT: L 22 LEU cc_start: 0.8235 (mm) cc_final: 0.7888 (mm) REVERT: L 25 ASN cc_start: 0.8380 (m110) cc_final: 0.7481 (m110) REVERT: L 39 ARG cc_start: 0.9344 (mmt180) cc_final: 0.8201 (mmt180) REVERT: L 66 ILE cc_start: 0.9821 (mp) cc_final: 0.9375 (tt) REVERT: L 67 ARG cc_start: 0.8925 (ttp80) cc_final: 0.7900 (ttp80) REVERT: L 72 TYR cc_start: 0.9283 (m-10) cc_final: 0.8795 (m-10) REVERT: L 85 ASP cc_start: 0.9082 (m-30) cc_final: 0.8501 (m-30) REVERT: M 57 TYR cc_start: 0.9054 (t80) cc_final: 0.8268 (t80) REVERT: M 87 VAL cc_start: 0.9278 (t) cc_final: 0.9063 (t) REVERT: M 94 ASN cc_start: 0.9532 (t0) cc_final: 0.9299 (t0) REVERT: M 99 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7798 (mmp80) REVERT: M 108 LEU cc_start: 0.9598 (pt) cc_final: 0.8989 (pp) REVERT: N 39 TYR cc_start: 0.7679 (t80) cc_final: 0.7395 (t80) REVERT: N 73 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8945 (mm-30) REVERT: N 81 ASN cc_start: 0.9069 (t160) cc_final: 0.8719 (t0) REVERT: N 92 GLN cc_start: 0.9195 (tt0) cc_final: 0.8669 (tm-30) REVERT: N 93 THR cc_start: 0.9399 (p) cc_final: 0.9076 (p) outliers start: 1 outliers final: 0 residues processed: 336 average time/residue: 0.1410 time to fit residues: 74.3520 Evaluate side-chains 294 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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: 7.9990 chunk 152 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 K 68 GLN L 27 GLN L 93 GLN N 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.108013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.068093 restraints weight = 92492.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070267 restraints weight = 46162.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071559 restraints weight = 28921.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072378 restraints weight = 21386.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072827 restraints weight = 17829.590| |-----------------------------------------------------------------------------| 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: 8 | |-----------------------------------------------------------------------------| |-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: 8 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.7489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 20565 Z= 0.256 Angle : 0.719 11.576 29072 Z= 0.400 Chirality : 0.044 0.265 3279 Planarity : 0.006 0.074 2665 Dihedral : 29.332 177.303 5081 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.20), residues: 1699 helix: 0.58 (0.20), residues: 585 sheet: -0.69 (0.27), residues: 372 loop : -1.60 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 190 TYR 0.034 0.002 TYR H 88 PHE 0.016 0.002 PHE M 25 TRP 0.026 0.002 TRP D 327 HIS 0.014 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00565 (20565) covalent geometry : angle 0.71881 (29072) hydrogen bonds : bond 0.08369 ( 1048) hydrogen bonds : angle 4.76143 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5352.51 seconds wall clock time: 92 minutes 29.91 seconds (5549.91 seconds total)