Starting phenix.real_space_refine on Mon Sep 14 16:42:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5m_21543/09_2026/6w5m_21543.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5m_21543/09_2026/6w5m_21543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5m_21543/09_2026/6w5m_21543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5m_21543/09_2026/6w5m_21543.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5m_21543/09_2026/6w5m_21543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5m_21543/09_2026/6w5m_21543.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15451 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 58 5.16 5 C 11457 2.51 5 N 3551 2.21 5 O 4216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19574 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2381 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain: "B" Number of atoms: 2302 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 2299 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 298, 2299 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2351 Chain: "C" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1185 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1742 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain breaks: 1 Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 4.15, per 1000 atoms: 0.21 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: 1.73 Conformation dependent library (CDL) restraints added in 648.2 milliseconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 35.6% alpha, 21.1% beta 156 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 3.03 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: 5.02 Time building geometry restraints manager: 2.31 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' DC P 111 " pdb=" O3' DC P 111 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" C3' DG P 84 " pdb=" C2' DG P 84 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG O 101 " pdb=" C2' DG O 101 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT P 57 " pdb=" C2' DT P 57 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA O 69 " pdb=" O3' DA O 69 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.88e+00 ... (remaining 20560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 28750 2.65 - 5.29: 308 5.29 - 7.94: 12 7.94 - 10.58: 0 10.58 - 13.23: 2 Bond angle restraints: 29072 Sorted by residual: angle pdb=" O4' DA P 14 " pdb=" C4' DA P 14 " pdb=" C3' DA P 14 " ideal model delta sigma weight residual 106.00 102.41 3.59 6.00e-01 2.78e+00 3.58e+01 angle pdb=" O4' DG P 130 " pdb=" C4' DG P 130 " pdb=" C3' DG P 130 " ideal model delta sigma weight residual 106.00 102.44 3.56 6.00e-01 2.78e+00 3.52e+01 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=" O5' DG P 112 " pdb=" C5' DG P 112 " pdb=" C4' DG P 112 " ideal model delta sigma weight residual 109.40 113.24 -3.84 8.00e-01 1.56e+00 2.30e+01 angle pdb=" O4' DA O 41 " pdb=" C4' DA O 41 " pdb=" C3' DA O 41 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 ... (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: 2562 0.057 - 0.115: 628 0.115 - 0.172: 82 0.172 - 0.230: 6 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: 2.380 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.270 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.006 0.050 20565 Z= 0.521 Angle : 0.785 13.229 29072 Z= 0.623 Chirality : 0.049 0.287 3279 Planarity : 0.005 0.078 2665 Dihedral : 25.405 175.923 8321 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 36.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.58 % Allowed : 6.66 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.18), residues: 1699 helix: -1.56 (0.19), residues: 578 sheet: -1.88 (0.24), residues: 373 loop : -2.25 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 42 TYR 0.016 0.002 TYR J 118 PHE 0.019 0.002 PHE D 484 TRP 0.021 0.002 TRP D 505 HIS 0.005 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.52 (20565) covalent geometry : angle 0.78458 / 0.62 (29072) hydrogen bonds : bond 0.19512 / 12.84 ( 1048) hydrogen bonds : angle 6.55139 / 4.47 ( 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 : 0.535 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 18 ASP cc_start: 0.1024 (t0) cc_final: 0.0774 (m-30) REVERT: A 80 LYS cc_start: 0.1410 (mmtt) cc_final: 0.0924 (mtmt) REVERT: A 137 LEU cc_start: 0.3783 (mt) cc_final: 0.3374 (mm) REVERT: A 213 PHE cc_start: 0.5150 (p90) cc_final: 0.4771 (p90) REVERT: A 247 ASP cc_start: 0.0822 (t0) cc_final: 0.0614 (t0) REVERT: C 3931 MET cc_start: -0.0630 (mtp) cc_final: -0.1037 (ttp) REVERT: D 288 LEU cc_start: 0.6546 (mt) cc_final: 0.6304 (mt) REVERT: D 336 MET cc_start: 0.4982 (tmm) cc_final: 0.3631 (mmt) REVERT: G 58 THR cc_start: 0.8511 (m) cc_final: 0.8174 (p) REVERT: G 65 LEU cc_start: 0.9331 (mt) cc_final: 0.8811 (mt) REVERT: G 73 GLU cc_start: 0.8546 (tt0) cc_final: 0.8231 (tm-30) REVERT: G 74 ILE cc_start: 0.9396 (mm) cc_final: 0.9192 (mm) REVERT: G 97 GLU cc_start: 0.9206 (mt-10) cc_final: 0.7137 (mt-10) REVERT: H 44 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8096 (mtmt) REVERT: H 67 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8269 (tmm-80) REVERT: I 17 ARG cc_start: 0.9024 (mtm180) cc_final: 0.8369 (ttm110) REVERT: I 32 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8346 (tpt170) REVERT: I 56 GLU cc_start: 0.9256 (tt0) cc_final: 0.8860 (tt0) REVERT: I 65 LEU cc_start: 0.9203 (mt) cc_final: 0.8889 (mt) REVERT: I 92 GLU cc_start: 0.8658 (mt-10) cc_final: 0.6044 (mt-10) REVERT: J 38 VAL cc_start: 0.9625 (m) cc_final: 0.9210 (m) REVERT: J 59 MET cc_start: 0.9238 (mmm) cc_final: 0.9024 (mmp) REVERT: J 83 ARG cc_start: 0.7558 (mtt90) cc_final: 0.7040 (mtt90) REVERT: J 96 ARG cc_start: 0.9142 (mtp180) cc_final: 0.8846 (ttm170) REVERT: J 103 LEU cc_start: 0.9424 (mt) cc_final: 0.8903 (mt) REVERT: K 59 GLU cc_start: 0.8256 (pm20) cc_final: 0.8018 (pm20) REVERT: K 73 GLU cc_start: 0.8644 (tt0) cc_final: 0.8442 (mt-10) REVERT: K 82 LEU cc_start: 0.8648 (mt) cc_final: 0.8444 (mm) REVERT: K 84 PHE cc_start: 0.8293 (m-80) cc_final: 0.7681 (m-80) REVERT: K 94 GLU cc_start: 0.9175 (tp30) cc_final: 0.8933 (tp30) REVERT: K 105 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8867 (tm-30) REVERT: K 120 MET cc_start: 0.8672 (tpp) cc_final: 0.7820 (mmm) 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: 0.9352 (tt) REVERT: L 81 VAL cc_start: 0.8556 (t) cc_final: 0.8310 (t) REVERT: M 23 LEU cc_start: 0.8292 (mt) cc_final: 0.7883 (mt) REVERT: M 56 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8173 (mt-10) REVERT: M 57 TYR cc_start: 0.9008 (t80) cc_final: 0.8279 (t80) REVERT: M 61 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8870 (mm-30) REVERT: M 65 LEU cc_start: 0.9414 (mt) cc_final: 0.9039 (mt) REVERT: M 68 ASN cc_start: 0.7909 (m-40) cc_final: 0.7518 (m-40) REVERT: M 87 VAL cc_start: 0.8959 (t) cc_final: 0.8502 (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 39 TYR cc_start: 0.7253 (t80) cc_final: 0.6666 (t80) REVERT: N 65 ASP cc_start: 0.9012 (t0) cc_final: 0.8659 (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: 0.8447 (tm-30) REVERT: N 117 LYS cc_start: 0.7177 (tttm) cc_final: 0.6820 (tttp) REVERT: N 118 TYR cc_start: 0.9123 (t80) cc_final: 0.8795 (t80) outliers start: 23 outliers final: 6 residues processed: 537 average time/residue: 0.1846 time to fit residues: 141.2890 Evaluate side-chains 352 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 345 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 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: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN B 170 HIS 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 323 ASN D 441 GLN G 39 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 89 ASN J 60 ASN J 79 HIS ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN K 68 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.115640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073395 restraints weight = 90296.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075616 restraints weight = 44983.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076955 restraints weight = 28337.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077768 restraints weight = 21005.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078194 restraints weight = 17392.197| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 20565 Z= 0.243 Angle : 0.811 10.139 29072 Z= 0.446 Chirality : 0.052 0.372 3279 Planarity : 0.007 0.065 2665 Dihedral : 29.896 178.326 5081 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.34 % Allowed : 5.70 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.19), residues: 1699 helix: -0.41 (0.19), residues: 599 sheet: -1.52 (0.26), residues: 369 loop : -1.73 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 129 TYR 0.031 0.003 TYR M 39 PHE 0.031 0.003 PHE G 67 TRP 0.024 0.002 TRP D 505 HIS 0.011 0.002 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.24 (20565) covalent geometry : angle 0.81141 / 0.45 (29072) hydrogen bonds : bond 0.09667 / 6.63 ( 1048) hydrogen bonds : angle 5.24894 / 3.62 ( 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 409 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 404 time to evaluate : 0.515 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: 0.0859 (t0) cc_final: 0.0515 (m-30) REVERT: A 80 LYS cc_start: 0.1277 (mmtt) cc_final: 0.0896 (mtmt) REVERT: A 134 MET cc_start: -0.0745 (mtm) cc_final: -0.1073 (mtm) REVERT: A 213 PHE cc_start: 0.5236 (p90) cc_final: 0.4517 (p90) REVERT: C 3931 MET cc_start: -0.0487 (mtp) cc_final: -0.0722 (ttp) REVERT: D 336 MET cc_start: 0.3955 (tmm) cc_final: 0.3241 (mmt) REVERT: G 65 LEU cc_start: 0.9457 (mt) cc_final: 0.9206 (mt) REVERT: G 73 GLU cc_start: 0.8549 (tt0) cc_final: 0.8333 (tm-30) REVERT: G 97 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8018 (mt-10) REVERT: G 119 ILE cc_start: 0.8254 (pt) cc_final: 0.7021 (pt) REVERT: G 120 MET cc_start: 0.8245 (tpt) cc_final: 0.7824 (mmm) REVERT: H 27 GLN cc_start: 0.8773 (pp30) cc_final: 0.8233 (pp30) REVERT: H 43 VAL cc_start: 0.9062 (p) cc_final: 0.8768 (m) REVERT: H 44 LYS cc_start: 0.9206 (mtpp) cc_final: 0.8815 (mmtm) REVERT: H 64 ASN cc_start: 0.9141 (m-40) cc_final: 0.8446 (m-40) REVERT: H 67 ARG cc_start: 0.9106 (ttp-110) cc_final: 0.8514 (ttp80) REVERT: H 68 ASP cc_start: 0.9232 (m-30) cc_final: 0.8985 (m-30) REVERT: H 75 HIS cc_start: 0.8016 (t-90) cc_final: 0.7757 (t-90) REVERT: H 88 TYR cc_start: 0.8822 (m-80) cc_final: 0.8621 (m-80) REVERT: I 32 ARG cc_start: 0.9047 (tmm-80) cc_final: 0.8612 (tpt170) REVERT: I 38 ASN cc_start: 0.9100 (m110) cc_final: 0.8812 (m-40) REVERT: I 42 ARG cc_start: 0.8651 (mtm180) cc_final: 0.8409 (mtm-85) REVERT: I 56 GLU cc_start: 0.8989 (tt0) cc_final: 0.8785 (tt0) REVERT: I 64 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8532 (tm-30) REVERT: I 90 ASP cc_start: 0.9093 (t0) cc_final: 0.8812 (t0) REVERT: I 92 GLU cc_start: 0.8102 (mt-10) cc_final: 0.6970 (mt-10) REVERT: I 99 ARG cc_start: 0.9045 (ptp90) cc_final: 0.8810 (mtm-85) REVERT: J 68 GLU cc_start: 0.8833 (tt0) cc_final: 0.8580 (tt0) REVERT: J 92 GLN cc_start: 0.9181 (pt0) cc_final: 0.8904 (pt0) REVERT: J 96 ARG cc_start: 0.9008 (mtp180) cc_final: 0.8661 (ttm110) REVERT: J 103 LEU cc_start: 0.9412 (mt) cc_final: 0.9001 (mt) REVERT: J 105 LYS cc_start: 0.9096 (pttp) cc_final: 0.8660 (pptt) REVERT: K 41 TYR cc_start: 0.6744 (m-80) cc_final: 0.6485 (m-80) REVERT: K 77 ASP cc_start: 0.9240 (t0) cc_final: 0.8993 (t70) REVERT: K 80 THR cc_start: 0.7927 (p) cc_final: 0.7396 (p) REVERT: K 82 LEU cc_start: 0.8813 (mt) cc_final: 0.8520 (mp) REVERT: K 84 PHE cc_start: 0.8564 (m-80) cc_final: 0.8210 (m-80) REVERT: K 97 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8854 (mt-10) REVERT: K 120 MET cc_start: 0.8789 (tpp) cc_final: 0.8458 (mtp) REVERT: K 122 LYS cc_start: 0.8606 (pttp) cc_final: 0.8171 (ptpt) REVERT: L 66 ILE cc_start: 0.9759 (OUTLIER) cc_final: 0.9336 (tt) REVERT: L 85 ASP cc_start: 0.8729 (m-30) cc_final: 0.8487 (m-30) REVERT: M 61 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8461 (mm-30) REVERT: M 65 LEU cc_start: 0.9659 (mt) cc_final: 0.9225 (mt) REVERT: M 79 ILE cc_start: 0.9198 (tp) cc_final: 0.8962 (mm) REVERT: M 87 VAL cc_start: 0.9107 (t) cc_final: 0.8812 (t) REVERT: M 88 ARG cc_start: 0.9266 (mmt180) cc_final: 0.8900 (mmp80) REVERT: M 91 GLU cc_start: 0.8759 (pm20) cc_final: 0.8545 (tm-30) REVERT: N 39 TYR cc_start: 0.7142 (t80) cc_final: 0.6657 (t80) REVERT: N 68 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8336 (mm-30) REVERT: N 76 ARG cc_start: 0.9116 (ttm-80) cc_final: 0.8474 (ttm170) REVERT: N 81 ASN cc_start: 0.8892 (t0) cc_final: 0.8442 (t0) REVERT: N 92 GLN cc_start: 0.8919 (tt0) cc_final: 0.8475 (tm-30) outliers start: 5 outliers final: 1 residues processed: 406 average time/residue: 0.1565 time to fit residues: 94.5337 Evaluate side-chains 340 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 4.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3839 HIS G 76 GLN G 93 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS K 39 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.111094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069301 restraints weight = 91230.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071419 restraints weight = 45090.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.072579 restraints weight = 28562.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073356 restraints weight = 21552.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073756 restraints weight = 18242.511| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 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 = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 20565 Z= 0.313 Angle : 0.842 11.195 29072 Z= 0.465 Chirality : 0.053 0.365 3279 Planarity : 0.007 0.061 2665 Dihedral : 29.810 175.030 5081 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.34 % Allowed : 4.67 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.19), residues: 1699 helix: -0.15 (0.20), residues: 591 sheet: -1.40 (0.25), residues: 374 loop : -1.64 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 343 TYR 0.029 0.003 TYR L 88 PHE 0.034 0.003 PHE G 78 TRP 0.024 0.002 TRP D 505 HIS 0.009 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.31 (20565) covalent geometry : angle 0.84197 / 0.47 (29072) hydrogen bonds : bond 0.10382 / 7.12 ( 1048) hydrogen bonds : angle 5.32860 / 3.67 ( 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 379 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 374 time to evaluate : 0.582 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 18 ASP cc_start: 0.1377 (t0) cc_final: 0.0938 (m-30) REVERT: A 80 LYS cc_start: 0.0842 (mmtt) cc_final: 0.0411 (mtmt) REVERT: A 213 PHE cc_start: 0.5283 (p90) cc_final: 0.4389 (p90) REVERT: C 3883 TYR cc_start: 0.4826 (m-80) cc_final: 0.4521 (m-80) REVERT: C 3884 MET cc_start: 0.1749 (ttp) cc_final: 0.1363 (tmm) REVERT: C 3894 ASP cc_start: 0.6390 (t70) cc_final: 0.6053 (t70) REVERT: C 3931 MET cc_start: -0.0614 (mtp) cc_final: -0.1124 (ttt) REVERT: D 336 MET cc_start: 0.3899 (tmm) cc_final: 0.3390 (mmt) REVERT: D 337 PRO cc_start: 0.2494 (Cg_exo) cc_final: 0.1844 (Cg_endo) REVERT: D 518 TYR cc_start: -0.1749 (t80) cc_final: -0.2115 (m-10) REVERT: G 50 GLU cc_start: 0.9310 (tp30) cc_final: 0.9064 (tp30) REVERT: G 65 LEU cc_start: 0.9544 (mt) cc_final: 0.9317 (mt) REVERT: G 104 PHE cc_start: 0.9484 (m-80) cc_final: 0.9253 (m-80) REVERT: G 119 ILE cc_start: 0.8382 (pt) cc_final: 0.7114 (pt) REVERT: G 120 MET cc_start: 0.8421 (tpt) cc_final: 0.8103 (mmm) REVERT: G 124 ILE cc_start: 0.9620 (pt) cc_final: 0.8676 (pt) REVERT: H 27 GLN cc_start: 0.8854 (pp30) cc_final: 0.8404 (pp30) REVERT: H 44 LYS cc_start: 0.9189 (mtpp) cc_final: 0.8935 (mmmm) REVERT: H 60 VAL cc_start: 0.9602 (p) cc_final: 0.9347 (p) REVERT: H 63 GLU cc_start: 0.9084 (tp30) cc_final: 0.8815 (tp30) REVERT: H 64 ASN cc_start: 0.9273 (m-40) cc_final: 0.8956 (m110) REVERT: H 67 ARG cc_start: 0.9212 (ttp-110) cc_final: 0.8979 (ttp-110) REVERT: H 75 HIS cc_start: 0.8330 (t-90) cc_final: 0.7951 (t-170) REVERT: H 88 TYR cc_start: 0.8957 (m-80) cc_final: 0.8539 (m-10) REVERT: I 32 ARG cc_start: 0.9009 (tmm-80) cc_final: 0.8657 (tpt170) REVERT: I 38 ASN cc_start: 0.9269 (m110) cc_final: 0.9010 (m-40) REVERT: I 50 TYR cc_start: 0.9365 (t80) cc_final: 0.9019 (t80) REVERT: I 64 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8620 (tm-30) REVERT: I 90 ASP cc_start: 0.9109 (t0) cc_final: 0.8804 (t0) REVERT: I 92 GLU cc_start: 0.8311 (mt-10) cc_final: 0.6748 (mt-10) REVERT: I 112 GLN cc_start: 0.7735 (mp10) cc_final: 0.7503 (mp10) REVERT: J 37 TYR cc_start: 0.9159 (m-80) cc_final: 0.8886 (m-80) REVERT: J 65 ASP cc_start: 0.9235 (t0) cc_final: 0.8965 (t0) REVERT: J 92 GLN cc_start: 0.9213 (tt0) cc_final: 0.8809 (tt0) REVERT: J 96 ARG cc_start: 0.9201 (mtp180) cc_final: 0.8946 (ttm110) REVERT: J 103 LEU cc_start: 0.9467 (mt) cc_final: 0.8930 (mt) REVERT: J 106 HIS cc_start: 0.8679 (m90) cc_final: 0.8121 (m170) REVERT: K 46 VAL cc_start: 0.9398 (t) cc_final: 0.9091 (t) REVERT: K 73 GLU cc_start: 0.8351 (tt0) cc_final: 0.8023 (tt0) REVERT: K 77 ASP cc_start: 0.9343 (t0) cc_final: 0.9052 (t70) REVERT: K 80 THR cc_start: 0.8261 (p) cc_final: 0.7604 (p) REVERT: K 81 ASP cc_start: 0.8597 (m-30) cc_final: 0.8244 (m-30) REVERT: K 82 LEU cc_start: 0.8693 (mt) cc_final: 0.8465 (mp) REVERT: K 84 PHE cc_start: 0.8657 (m-80) cc_final: 0.8109 (m-80) REVERT: K 85 GLN cc_start: 0.9052 (mp-120) cc_final: 0.8710 (mm-40) REVERT: K 93 GLN cc_start: 0.8551 (pp30) cc_final: 0.7800 (tm-30) REVERT: K 94 GLU cc_start: 0.9006 (tp30) cc_final: 0.8788 (tp30) REVERT: K 105 GLU cc_start: 0.9271 (tt0) cc_final: 0.8987 (tm-30) REVERT: K 125 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: L 25 ASN cc_start: 0.8343 (m-40) cc_final: 0.7272 (m110) REVERT: L 39 ARG cc_start: 0.9114 (mmt180) cc_final: 0.8903 (mmm160) REVERT: L 45 ARG cc_start: 0.9079 (tpp80) cc_final: 0.8696 (tpp80) REVERT: L 66 ILE cc_start: 0.9763 (OUTLIER) cc_final: 0.9543 (tt) REVERT: L 67 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8788 (ttp80) REVERT: L 75 HIS cc_start: 0.9025 (t-90) cc_final: 0.8804 (t70) REVERT: L 85 ASP cc_start: 0.9022 (m-30) cc_final: 0.8707 (m-30) REVERT: L 98 TYR cc_start: 0.8534 (m-10) cc_final: 0.8049 (m-80) REVERT: M 57 TYR cc_start: 0.9351 (t80) cc_final: 0.8642 (t80) REVERT: M 65 LEU cc_start: 0.9563 (mt) cc_final: 0.9329 (mt) REVERT: M 68 ASN cc_start: 0.8598 (m110) cc_final: 0.7971 (m110) REVERT: M 88 ARG cc_start: 0.9366 (mmt180) cc_final: 0.8956 (mmp80) REVERT: N 30 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7508 (mtt180) REVERT: N 39 TYR cc_start: 0.7376 (t80) cc_final: 0.6887 (t80) REVERT: N 68 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8376 (mm-30) REVERT: N 76 ARG cc_start: 0.9066 (ttm-80) cc_final: 0.8740 (ttm170) REVERT: N 81 ASN cc_start: 0.8733 (t0) cc_final: 0.8329 (t0) REVERT: N 92 GLN cc_start: 0.9197 (tt0) cc_final: 0.8741 (tm-30) outliers start: 5 outliers final: 0 residues processed: 376 average time/residue: 0.1518 time to fit residues: 86.0368 Evaluate side-chains 327 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 9.9990 chunk 189 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN K 85 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.108072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.066650 restraints weight = 92430.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068603 restraints weight = 46967.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069771 restraints weight = 30193.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070520 restraints weight = 22927.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070971 restraints weight = 19444.569| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.177 20565 Z= 0.351 Angle : 0.899 11.560 29072 Z= 0.490 Chirality : 0.055 0.369 3279 Planarity : 0.007 0.057 2665 Dihedral : 29.936 175.431 5081 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.14 % Allowed : 4.74 % 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 are not related in a simple way. whole: -1.84 (0.19), residues: 1699 helix: -0.54 (0.19), residues: 588 sheet: -1.23 (0.25), residues: 381 loop : -1.68 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG J 83 TYR 0.025 0.003 TYR D 328 PHE 0.036 0.003 PHE D 464 TRP 0.024 0.002 TRP D 505 HIS 0.012 0.002 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.35 (20565) covalent geometry : angle 0.89872 / 0.49 (29072) hydrogen bonds : bond 0.10985 / 7.47 ( 1048) hydrogen bonds : angle 5.56084 / 3.83 ( 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 371 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 0.565 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: A 18 ASP cc_start: 0.1947 (t0) cc_final: 0.1646 (m-30) REVERT: A 80 LYS cc_start: 0.0718 (mmtt) cc_final: 0.0206 (mtmt) REVERT: A 175 ILE cc_start: 0.1520 (mt) cc_final: 0.1261 (mt) REVERT: A 213 PHE cc_start: 0.5218 (p90) cc_final: 0.4345 (p90) REVERT: C 3883 TYR cc_start: 0.4557 (m-80) cc_final: 0.4141 (m-80) REVERT: D 336 MET cc_start: 0.3605 (tmm) cc_final: 0.3223 (mmt) REVERT: D 337 PRO cc_start: 0.3042 (Cg_exo) cc_final: 0.2434 (Cg_endo) REVERT: G 65 LEU cc_start: 0.9570 (mt) cc_final: 0.9370 (mt) REVERT: G 110 CYS cc_start: 0.8934 (m) cc_final: 0.8702 (m) REVERT: G 113 HIS cc_start: 0.8836 (t70) cc_final: 0.8373 (t70) REVERT: G 120 MET cc_start: 0.8684 (tpt) cc_final: 0.8112 (mmm) REVERT: H 27 GLN cc_start: 0.8955 (pp30) cc_final: 0.8686 (pp30) REVERT: H 64 ASN cc_start: 0.9430 (m-40) cc_final: 0.9222 (m110) REVERT: H 65 VAL cc_start: 0.9799 (m) cc_final: 0.9590 (p) REVERT: H 75 HIS cc_start: 0.8681 (t-90) cc_final: 0.8309 (t-90) REVERT: H 88 TYR cc_start: 0.9074 (m-80) cc_final: 0.8692 (m-10) REVERT: I 25 PHE cc_start: 0.9174 (m-10) cc_final: 0.8933 (m-10) REVERT: I 32 ARG cc_start: 0.8905 (tmm-80) cc_final: 0.8653 (tpt170) REVERT: I 50 TYR cc_start: 0.9445 (t80) cc_final: 0.9204 (t80) REVERT: I 64 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8632 (tm-30) REVERT: I 77 ARG cc_start: 0.8953 (mtm110) cc_final: 0.8675 (mtm180) REVERT: I 84 GLN cc_start: 0.9536 (tp40) cc_final: 0.9184 (tp-100) REVERT: I 90 ASP cc_start: 0.9149 (t0) cc_final: 0.8777 (t0) REVERT: I 112 GLN cc_start: 0.7921 (mp10) cc_final: 0.7544 (mp10) REVERT: J 57 SER cc_start: 0.9531 (m) cc_final: 0.9302 (p) REVERT: J 65 ASP cc_start: 0.9180 (t0) cc_final: 0.8932 (t0) REVERT: J 81 ASN cc_start: 0.9176 (t0) cc_final: 0.8786 (t0) REVERT: J 96 ARG cc_start: 0.9247 (mtp180) cc_final: 0.8907 (ttm110) REVERT: J 106 HIS cc_start: 0.8800 (m90) cc_final: 0.8502 (m90) REVERT: K 73 GLU cc_start: 0.8392 (tt0) cc_final: 0.7720 (tt0) REVERT: K 80 THR cc_start: 0.8397 (p) cc_final: 0.7705 (p) REVERT: K 81 ASP cc_start: 0.8608 (m-30) cc_final: 0.8273 (m-30) REVERT: K 85 GLN cc_start: 0.9210 (mp10) cc_final: 0.8740 (mm110) REVERT: K 93 GLN cc_start: 0.8756 (pp30) cc_final: 0.8080 (tm-30) REVERT: K 105 GLU cc_start: 0.9319 (tt0) cc_final: 0.8919 (pp20) REVERT: L 25 ASN cc_start: 0.8534 (m-40) cc_final: 0.7460 (m110) REVERT: L 36 ARG cc_start: 0.9078 (mtp180) cc_final: 0.8746 (ttp-110) REVERT: L 45 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8702 (tpp80) REVERT: L 84 MET cc_start: 0.8948 (mpp) cc_final: 0.8560 (mmm) REVERT: L 88 TYR cc_start: 0.8703 (m-10) cc_final: 0.8075 (m-80) REVERT: L 98 TYR cc_start: 0.8419 (m-10) cc_final: 0.8025 (m-80) REVERT: M 57 TYR cc_start: 0.9298 (t80) cc_final: 0.8594 (t80) REVERT: M 68 ASN cc_start: 0.8550 (m110) cc_final: 0.8031 (m110) REVERT: M 92 GLU cc_start: 0.8929 (tt0) cc_final: 0.8596 (tt0) REVERT: M 100 VAL cc_start: 0.9488 (t) cc_final: 0.9158 (t) REVERT: N 30 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7133 (tpp80) REVERT: N 39 TYR cc_start: 0.7590 (t80) cc_final: 0.6975 (t80) REVERT: N 56 MET cc_start: 0.9123 (ptp) cc_final: 0.8837 (ptp) REVERT: N 68 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8408 (mm-30) REVERT: N 81 ASN cc_start: 0.8906 (t0) cc_final: 0.8457 (t0) REVERT: N 92 GLN cc_start: 0.9193 (tt0) cc_final: 0.8556 (tm-30) REVERT: N 93 THR cc_start: 0.9418 (p) cc_final: 0.9096 (p) outliers start: 2 outliers final: 0 residues processed: 369 average time/residue: 0.1433 time to fit residues: 80.1585 Evaluate side-chains 315 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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: 5.9990 chunk 153 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 177 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS K 39 HIS K 68 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN L 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.110764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068965 restraints weight = 90951.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071001 restraints weight = 44972.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072257 restraints weight = 28554.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073047 restraints weight = 21657.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073461 restraints weight = 18286.525| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20565 Z= 0.217 Angle : 0.767 9.230 29072 Z= 0.424 Chirality : 0.050 0.371 3279 Planarity : 0.006 0.056 2665 Dihedral : 29.950 175.923 5081 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 1699 helix: 0.05 (0.20), residues: 590 sheet: -1.11 (0.25), residues: 370 loop : -1.48 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 39 TYR 0.043 0.003 TYR H 88 PHE 0.018 0.002 PHE G 78 TRP 0.033 0.002 TRP A 279 HIS 0.008 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.22 (20565) covalent geometry : angle 0.76706 / 0.42 (29072) hydrogen bonds : bond 0.09086 / 6.32 ( 1048) hydrogen bonds : angle 5.04769 / 3.47 ( 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 382 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.517 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 18 ASP cc_start: 0.2096 (t0) cc_final: 0.1774 (m-30) REVERT: A 61 ILE cc_start: 0.1684 (mm) cc_final: 0.1126 (pt) REVERT: A 80 LYS cc_start: 0.0874 (mmtt) cc_final: 0.0361 (mtmt) REVERT: A 134 MET cc_start: -0.1563 (mtm) cc_final: -0.1784 (mtm) REVERT: A 175 ILE cc_start: 0.1316 (mt) cc_final: 0.1050 (mt) REVERT: A 213 PHE cc_start: 0.5339 (p90) cc_final: 0.4618 (p90) REVERT: C 3883 TYR cc_start: 0.4644 (m-80) cc_final: 0.4290 (m-80) REVERT: C 3931 MET cc_start: -0.1294 (mtt) cc_final: -0.2290 (ttt) REVERT: D 336 MET cc_start: 0.3727 (tmm) cc_final: 0.3206 (mmt) REVERT: D 337 PRO cc_start: 0.2363 (Cg_exo) cc_final: 0.1746 (Cg_endo) REVERT: G 119 ILE cc_start: 0.8609 (pt) cc_final: 0.7121 (pt) REVERT: G 120 MET cc_start: 0.8615 (tpt) cc_final: 0.8153 (mmm) REVERT: H 27 GLN cc_start: 0.8917 (pp30) cc_final: 0.8599 (pp30) REVERT: H 29 ILE cc_start: 0.9285 (mm) cc_final: 0.9009 (pt) REVERT: H 39 ARG cc_start: 0.9051 (mmp80) cc_final: 0.8702 (mmp-170) REVERT: H 64 ASN cc_start: 0.9554 (m-40) cc_final: 0.9274 (m110) REVERT: H 88 TYR cc_start: 0.8771 (m-80) cc_final: 0.8282 (m-10) REVERT: H 98 TYR cc_start: 0.8978 (m-80) cc_final: 0.8765 (m-80) REVERT: I 61 GLU cc_start: 0.8415 (mp0) cc_final: 0.8016 (mp0) REVERT: I 64 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8725 (tm-30) REVERT: I 77 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8701 (mtm180) REVERT: I 84 GLN cc_start: 0.9480 (tp40) cc_final: 0.9131 (tp-100) REVERT: I 90 ASP cc_start: 0.9064 (t0) cc_final: 0.8714 (t0) REVERT: I 92 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7752 (mt-10) REVERT: J 57 SER cc_start: 0.9418 (m) cc_final: 0.9162 (p) REVERT: J 58 ILE cc_start: 0.9410 (mm) cc_final: 0.9169 (mm) REVERT: J 81 ASN cc_start: 0.9170 (t0) cc_final: 0.8688 (t0) REVERT: J 83 ARG cc_start: 0.8855 (mtp180) cc_final: 0.8400 (mtp-110) REVERT: J 96 ARG cc_start: 0.9177 (mtp180) cc_final: 0.8744 (ttm110) REVERT: J 103 LEU cc_start: 0.9625 (mt) cc_final: 0.9394 (mt) REVERT: J 105 LYS cc_start: 0.9029 (ptmm) cc_final: 0.8707 (ptmm) REVERT: J 106 HIS cc_start: 0.8673 (m90) cc_final: 0.8222 (m90) REVERT: K 61 LEU cc_start: 0.9360 (mp) cc_final: 0.9077 (mp) REVERT: K 73 GLU cc_start: 0.8262 (tt0) cc_final: 0.7628 (tt0) REVERT: K 77 ASP cc_start: 0.9297 (t0) cc_final: 0.9087 (t70) REVERT: K 80 THR cc_start: 0.8430 (p) cc_final: 0.7590 (p) REVERT: K 81 ASP cc_start: 0.8451 (m-30) cc_final: 0.8177 (m-30) REVERT: K 84 PHE cc_start: 0.8709 (m-80) cc_final: 0.8201 (m-80) REVERT: K 85 GLN cc_start: 0.9246 (mp10) cc_final: 0.8990 (mm110) REVERT: K 97 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8059 (mm-30) REVERT: K 105 GLU cc_start: 0.9249 (tt0) cc_final: 0.8920 (pp20) REVERT: K 110 CYS cc_start: 0.8762 (t) cc_final: 0.8557 (t) REVERT: K 117 VAL cc_start: 0.9214 (m) cc_final: 0.8935 (p) REVERT: K 131 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8559 (mtm-85) REVERT: L 22 LEU cc_start: 0.8417 (mm) cc_final: 0.7977 (mm) REVERT: L 25 ASN cc_start: 0.8447 (m-40) cc_final: 0.7535 (m110) REVERT: L 63 GLU cc_start: 0.8818 (tp30) cc_final: 0.8588 (tp30) REVERT: L 84 MET cc_start: 0.8755 (mpp) cc_final: 0.8425 (mmm) REVERT: L 85 ASP cc_start: 0.9226 (m-30) cc_final: 0.8957 (m-30) REVERT: L 88 TYR cc_start: 0.8660 (m-80) cc_final: 0.7843 (m-10) REVERT: L 98 TYR cc_start: 0.8204 (m-10) cc_final: 0.7936 (m-80) REVERT: M 35 ARG cc_start: 0.9269 (mtm180) cc_final: 0.9009 (mtm110) REVERT: M 57 TYR cc_start: 0.9362 (t80) cc_final: 0.8416 (t80) REVERT: M 68 ASN cc_start: 0.8630 (m110) cc_final: 0.8061 (m110) REVERT: M 88 ARG cc_start: 0.9320 (mmt180) cc_final: 0.9046 (mmp80) REVERT: N 30 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7285 (mtt180) REVERT: N 39 TYR cc_start: 0.7437 (t80) cc_final: 0.6904 (t80) REVERT: N 65 ASP cc_start: 0.8963 (t70) cc_final: 0.8690 (t0) REVERT: N 81 ASN cc_start: 0.8864 (t0) cc_final: 0.8447 (t0) REVERT: N 92 GLN cc_start: 0.9185 (tt0) cc_final: 0.8518 (tm-30) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.1477 time to fit residues: 84.7267 Evaluate side-chains 310 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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: 7.9990 chunk 185 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 143 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 156 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 overall best weight: 2.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN K 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.111402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069609 restraints weight = 89593.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071697 restraints weight = 44017.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072975 restraints weight = 27839.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.073795 restraints weight = 20901.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074205 restraints weight = 17630.883| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20565 Z= 0.192 Angle : 0.754 10.317 29072 Z= 0.416 Chirality : 0.050 0.372 3279 Planarity : 0.006 0.060 2665 Dihedral : 29.859 176.007 5081 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.19), residues: 1699 helix: 0.39 (0.20), residues: 588 sheet: -1.01 (0.26), residues: 361 loop : -1.42 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 39 TYR 0.029 0.003 TYR D 518 PHE 0.018 0.002 PHE D 488 TRP 0.025 0.002 TRP A 279 HIS 0.008 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (20565) covalent geometry : angle 0.75447 / 0.42 (29072) hydrogen bonds : bond 0.08682 / 6.06 ( 1048) hydrogen bonds : angle 4.89546 / 3.36 ( 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 366 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.561 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: 0.1414 (mm) cc_final: 0.0895 (pt) REVERT: A 80 LYS cc_start: 0.1031 (mmtt) cc_final: 0.0499 (mtmt) REVERT: A 134 MET cc_start: -0.1599 (mtm) cc_final: -0.1822 (mtm) REVERT: A 213 PHE cc_start: 0.5249 (p90) cc_final: 0.4442 (p90) REVERT: C 3931 MET cc_start: -0.1381 (mtt) cc_final: -0.2397 (ttt) REVERT: D 336 MET cc_start: 0.3716 (tmm) cc_final: 0.3192 (mmt) REVERT: D 337 PRO cc_start: 0.2242 (Cg_exo) cc_final: 0.1629 (Cg_endo) REVERT: G 50 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8737 (mt-10) REVERT: G 58 THR cc_start: 0.9355 (p) cc_final: 0.9126 (p) REVERT: G 59 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8566 (mm-30) REVERT: G 61 LEU cc_start: 0.9064 (mm) cc_final: 0.8662 (mm) REVERT: G 65 LEU cc_start: 0.9480 (mt) cc_final: 0.9104 (mm) REVERT: G 97 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8356 (mm-30) REVERT: G 104 PHE cc_start: 0.9458 (m-80) cc_final: 0.9051 (m-80) REVERT: G 119 ILE cc_start: 0.8572 (pt) cc_final: 0.7211 (pt) REVERT: G 120 MET cc_start: 0.8593 (tpt) cc_final: 0.8130 (mmm) REVERT: G 133 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7284 (mp0) REVERT: H 27 GLN cc_start: 0.8866 (pp30) cc_final: 0.8400 (pp30) REVERT: H 29 ILE cc_start: 0.9323 (mm) cc_final: 0.9121 (pt) REVERT: H 39 ARG cc_start: 0.9267 (mmp80) cc_final: 0.8785 (mmt-90) REVERT: H 64 ASN cc_start: 0.9459 (m-40) cc_final: 0.9242 (m110) REVERT: H 73 THR cc_start: 0.9703 (m) cc_final: 0.9440 (p) REVERT: H 74 GLU cc_start: 0.8184 (tp30) cc_final: 0.7880 (tp30) REVERT: I 38 ASN cc_start: 0.9314 (m110) cc_final: 0.9098 (m110) REVERT: I 50 TYR cc_start: 0.9327 (t80) cc_final: 0.8431 (t80) REVERT: I 64 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8599 (tm-30) REVERT: I 77 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8703 (mtm180) REVERT: I 84 GLN cc_start: 0.9438 (tp40) cc_final: 0.9123 (tp-100) REVERT: I 90 ASP cc_start: 0.8990 (t0) cc_final: 0.8548 (t0) REVERT: I 92 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7537 (mt-10) REVERT: I 104 GLN cc_start: 0.8948 (mp10) cc_final: 0.8284 (mp10) REVERT: J 57 SER cc_start: 0.9391 (m) cc_final: 0.9161 (p) REVERT: J 68 GLU cc_start: 0.8825 (tt0) cc_final: 0.8553 (tt0) REVERT: J 81 ASN cc_start: 0.9217 (t0) cc_final: 0.8680 (t0) REVERT: J 83 ARG cc_start: 0.8868 (mtp180) cc_final: 0.8178 (mtp180) REVERT: J 92 GLN cc_start: 0.9335 (tt0) cc_final: 0.8044 (tp40) REVERT: J 96 ARG cc_start: 0.9117 (mtp180) cc_final: 0.8828 (ttm110) REVERT: J 103 LEU cc_start: 0.9541 (mt) cc_final: 0.9279 (mt) REVERT: J 106 HIS cc_start: 0.8642 (m90) cc_final: 0.8259 (m170) REVERT: K 50 GLU cc_start: 0.8947 (tp30) cc_final: 0.8734 (tp30) REVERT: K 61 LEU cc_start: 0.9087 (mp) cc_final: 0.8801 (mp) REVERT: K 62 ILE cc_start: 0.9594 (pt) cc_final: 0.9003 (pt) REVERT: K 73 GLU cc_start: 0.8243 (tt0) cc_final: 0.7646 (tt0) REVERT: K 77 ASP cc_start: 0.9339 (t0) cc_final: 0.9118 (t70) REVERT: K 80 THR cc_start: 0.8368 (p) cc_final: 0.7675 (p) REVERT: K 81 ASP cc_start: 0.8454 (m-30) cc_final: 0.8216 (m-30) REVERT: K 84 PHE cc_start: 0.8637 (m-80) cc_final: 0.8191 (m-80) REVERT: K 85 GLN cc_start: 0.9251 (mp10) cc_final: 0.9038 (mm-40) REVERT: K 97 GLU cc_start: 0.9018 (mt-10) cc_final: 0.7919 (mm-30) REVERT: K 105 GLU cc_start: 0.9299 (tt0) cc_final: 0.8935 (pp20) REVERT: K 110 CYS cc_start: 0.8761 (t) cc_final: 0.8532 (t) REVERT: K 117 VAL cc_start: 0.9253 (m) cc_final: 0.8977 (p) REVERT: L 22 LEU cc_start: 0.8236 (mm) cc_final: 0.7689 (mm) REVERT: L 25 ASN cc_start: 0.8490 (m-40) cc_final: 0.7580 (m110) REVERT: L 84 MET cc_start: 0.8725 (mpp) cc_final: 0.8143 (mpp) REVERT: L 85 ASP cc_start: 0.9187 (m-30) cc_final: 0.8937 (m-30) REVERT: L 88 TYR cc_start: 0.8692 (m-10) cc_final: 0.8162 (m-80) REVERT: M 57 TYR cc_start: 0.9368 (t80) cc_final: 0.8429 (t80) REVERT: M 68 ASN cc_start: 0.8643 (m110) cc_final: 0.8015 (m110) REVERT: M 88 ARG cc_start: 0.9195 (mmt180) cc_final: 0.8964 (mmp80) REVERT: M 92 GLU cc_start: 0.8964 (tt0) cc_final: 0.8562 (tt0) REVERT: N 30 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7233 (mtt180) REVERT: N 39 TYR cc_start: 0.7465 (t80) cc_final: 0.7128 (t80) REVERT: N 81 ASN cc_start: 0.8877 (t0) cc_final: 0.8441 (t0) REVERT: N 92 GLN cc_start: 0.9232 (tt0) cc_final: 0.8536 (tm-30) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.1281 time to fit residues: 73.7987 Evaluate side-chains 313 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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: 8.9990 chunk 66 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN K 68 GLN K 108 ASN L 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.113105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071106 restraints weight = 90741.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073283 restraints weight = 45121.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.074565 restraints weight = 28327.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075403 restraints weight = 21080.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.075901 restraints weight = 17646.836| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20565 Z= 0.156 Angle : 0.730 9.918 29072 Z= 0.402 Chirality : 0.049 0.376 3279 Planarity : 0.006 0.100 2665 Dihedral : 29.721 176.881 5081 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.14 % Allowed : 2.13 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.19), residues: 1699 helix: 0.59 (0.20), residues: 588 sheet: -1.01 (0.26), residues: 360 loop : -1.40 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 190 TYR 0.030 0.002 TYR H 98 PHE 0.025 0.002 PHE I 25 TRP 0.025 0.002 TRP A 279 HIS 0.017 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (20565) covalent geometry : angle 0.73005 / 0.40 (29072) hydrogen bonds : bond 0.08216 / 5.78 ( 1048) hydrogen bonds : angle 4.70957 / 3.25 ( 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 378 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 0.585 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: 0.1551 (mm) cc_final: 0.1093 (pt) REVERT: A 80 LYS cc_start: 0.1090 (mmtt) cc_final: 0.0578 (mtmt) REVERT: A 213 PHE cc_start: 0.5049 (p90) cc_final: 0.4367 (p90) REVERT: C 3931 MET cc_start: -0.1387 (mtt) cc_final: -0.2177 (ttt) REVERT: D 336 MET cc_start: 0.4316 (tmm) cc_final: 0.3253 (mmt) REVERT: D 337 PRO cc_start: 0.1830 (Cg_exo) cc_final: 0.1214 (Cg_endo) REVERT: G 51 ILE cc_start: 0.9389 (mt) cc_final: 0.9182 (mt) REVERT: G 58 THR cc_start: 0.9320 (p) cc_final: 0.9038 (p) REVERT: G 59 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8469 (mm-30) REVERT: G 65 LEU cc_start: 0.9451 (mt) cc_final: 0.9124 (mm) REVERT: G 120 MET cc_start: 0.8606 (tpt) cc_final: 0.8142 (mmm) REVERT: G 133 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7316 (mp0) REVERT: H 27 GLN cc_start: 0.8836 (pp30) cc_final: 0.8388 (pp30) REVERT: H 29 ILE cc_start: 0.9354 (mm) cc_final: 0.9154 (pt) REVERT: H 44 LYS cc_start: 0.9338 (mmmt) cc_final: 0.8948 (mmtt) REVERT: H 73 THR cc_start: 0.9707 (m) cc_final: 0.9414 (p) REVERT: H 74 GLU cc_start: 0.8109 (tp30) cc_final: 0.7680 (tp30) REVERT: H 88 TYR cc_start: 0.8836 (m-10) cc_final: 0.8558 (m-10) REVERT: I 38 ASN cc_start: 0.9277 (m110) cc_final: 0.9015 (m110) REVERT: I 64 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8580 (tm-30) REVERT: I 90 ASP cc_start: 0.8853 (t0) cc_final: 0.8440 (t0) REVERT: I 104 GLN cc_start: 0.8957 (mp10) cc_final: 0.8324 (mp10) REVERT: J 57 SER cc_start: 0.9378 (m) cc_final: 0.9108 (p) REVERT: J 81 ASN cc_start: 0.9224 (t0) cc_final: 0.8604 (t0) REVERT: J 83 ARG cc_start: 0.8869 (mtp180) cc_final: 0.8296 (mtp-110) REVERT: J 96 ARG cc_start: 0.9093 (mtp180) cc_final: 0.8738 (ttm110) REVERT: J 106 HIS cc_start: 0.8789 (m90) cc_final: 0.8206 (m170) REVERT: K 62 ILE cc_start: 0.9591 (pt) cc_final: 0.9325 (pt) REVERT: K 73 GLU cc_start: 0.8251 (tt0) cc_final: 0.7611 (tt0) REVERT: K 80 THR cc_start: 0.8393 (p) cc_final: 0.7604 (p) REVERT: K 81 ASP cc_start: 0.8264 (m-30) cc_final: 0.8035 (m-30) REVERT: K 84 PHE cc_start: 0.8615 (m-80) cc_final: 0.8188 (m-80) REVERT: K 85 GLN cc_start: 0.9207 (mp10) cc_final: 0.8925 (mm110) REVERT: K 93 GLN cc_start: 0.8894 (pp30) cc_final: 0.8299 (pp30) REVERT: K 97 GLU cc_start: 0.9042 (mt-10) cc_final: 0.7986 (mm-30) REVERT: K 99 TYR cc_start: 0.8673 (t80) cc_final: 0.8236 (t80) REVERT: K 105 GLU cc_start: 0.9330 (tt0) cc_final: 0.8919 (pp20) REVERT: K 110 CYS cc_start: 0.8926 (t) cc_final: 0.8604 (t) REVERT: K 117 VAL cc_start: 0.9231 (m) cc_final: 0.8868 (p) REVERT: L 22 LEU cc_start: 0.8268 (mm) cc_final: 0.7754 (mm) REVERT: L 25 ASN cc_start: 0.8493 (m-40) cc_final: 0.7741 (m110) REVERT: L 45 ARG cc_start: 0.9208 (tpp80) cc_final: 0.8355 (tpp80) REVERT: L 84 MET cc_start: 0.8612 (mpp) cc_final: 0.8002 (mpp) REVERT: L 85 ASP cc_start: 0.9190 (m-30) cc_final: 0.8905 (m-30) REVERT: L 88 TYR cc_start: 0.8758 (m-10) cc_final: 0.8270 (m-80) REVERT: L 98 TYR cc_start: 0.7979 (m-80) cc_final: 0.7373 (m-80) REVERT: M 57 TYR cc_start: 0.9258 (t80) cc_final: 0.8369 (t80) REVERT: M 64 GLU cc_start: 0.8868 (pp20) cc_final: 0.8543 (pp20) REVERT: M 68 ASN cc_start: 0.8712 (m110) cc_final: 0.8482 (m110) REVERT: M 72 ASP cc_start: 0.8498 (m-30) cc_final: 0.7900 (t70) REVERT: M 87 VAL cc_start: 0.9362 (t) cc_final: 0.8892 (t) REVERT: M 88 ARG cc_start: 0.9204 (mmt180) cc_final: 0.8878 (mmp80) REVERT: N 30 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7591 (ttm170) REVERT: N 68 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8267 (mm-30) REVERT: N 81 ASN cc_start: 0.8882 (t0) cc_final: 0.8422 (t0) REVERT: N 92 GLN cc_start: 0.9241 (tt0) cc_final: 0.8505 (tm-30) outliers start: 2 outliers final: 1 residues processed: 377 average time/residue: 0.1315 time to fit residues: 76.8725 Evaluate side-chains 324 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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: 10.0000 chunk 0 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 51 optimal weight: 40.0000 chunk 131 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS K 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.109883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068638 restraints weight = 91528.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070753 restraints weight = 45673.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072023 restraints weight = 28785.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072806 restraints weight = 21449.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073278 restraints weight = 17998.134| |-----------------------------------------------------------------------------| 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: 10 | |-----------------------------------------------------------------------------| |-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: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5374 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= 0.251 Angle : 0.773 11.398 29072 Z= 0.426 Chirality : 0.050 0.361 3279 Planarity : 0.006 0.087 2665 Dihedral : 29.680 175.550 5081 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1699 helix: 0.36 (0.20), residues: 588 sheet: -0.98 (0.26), residues: 360 loop : -1.44 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 77 TYR 0.025 0.002 TYR H 98 PHE 0.022 0.002 PHE I 25 TRP 0.022 0.002 TRP D 327 HIS 0.008 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.25 (20565) covalent geometry : angle 0.77251 / 0.43 (29072) hydrogen bonds : bond 0.08983 / 6.20 ( 1048) hydrogen bonds : angle 4.94167 / 3.41 ( 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 348 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.580 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: 0.0820 (mm) cc_final: 0.0336 (pt) REVERT: A 80 LYS cc_start: 0.1126 (mmtt) cc_final: 0.0593 (mtmt) REVERT: A 213 PHE cc_start: 0.5121 (p90) cc_final: 0.4410 (p90) REVERT: C 3931 MET cc_start: -0.1411 (mtt) cc_final: -0.2187 (ttt) REVERT: D 336 MET cc_start: 0.5078 (tmm) cc_final: 0.3511 (mmt) REVERT: G 60 LEU cc_start: 0.8955 (pt) cc_final: 0.7829 (pp) REVERT: G 61 LEU cc_start: 0.9272 (mm) cc_final: 0.8789 (mm) REVERT: G 65 LEU cc_start: 0.9522 (mt) cc_final: 0.9253 (mm) REVERT: G 93 GLN cc_start: 0.8796 (pp30) cc_final: 0.8347 (pp30) REVERT: G 104 PHE cc_start: 0.9521 (m-80) cc_final: 0.9301 (m-80) REVERT: G 120 MET cc_start: 0.8705 (tpt) cc_final: 0.8213 (mmm) REVERT: G 133 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7239 (mp0) REVERT: H 27 GLN cc_start: 0.8923 (pp30) cc_final: 0.8653 (pp30) REVERT: H 29 ILE cc_start: 0.9364 (mm) cc_final: 0.9150 (pt) REVERT: H 44 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9042 (mmtt) REVERT: H 63 GLU cc_start: 0.8924 (tp30) cc_final: 0.8653 (tp30) REVERT: H 73 THR cc_start: 0.9721 (m) cc_final: 0.9489 (p) REVERT: H 74 GLU cc_start: 0.8081 (tp30) cc_final: 0.7700 (tp30) REVERT: I 38 ASN cc_start: 0.9353 (m110) cc_final: 0.9144 (m110) REVERT: I 61 GLU cc_start: 0.8538 (mp0) cc_final: 0.8123 (mp0) REVERT: I 64 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8663 (tm-30) REVERT: I 90 ASP cc_start: 0.9145 (t0) cc_final: 0.8550 (t70) REVERT: I 104 GLN cc_start: 0.8964 (mp10) cc_final: 0.8367 (mp10) REVERT: J 57 SER cc_start: 0.9475 (m) cc_final: 0.9239 (p) REVERT: J 68 GLU cc_start: 0.8775 (tt0) cc_final: 0.8552 (tt0) REVERT: J 81 ASN cc_start: 0.9289 (t0) cc_final: 0.8756 (t0) REVERT: J 83 ARG cc_start: 0.8957 (mtp180) cc_final: 0.8125 (mtp180) REVERT: J 96 ARG cc_start: 0.9198 (mtp180) cc_final: 0.8793 (ttm110) REVERT: J 102 GLU cc_start: 0.9048 (pm20) cc_final: 0.8390 (pm20) REVERT: J 103 LEU cc_start: 0.9401 (mp) cc_final: 0.8939 (mp) REVERT: J 106 HIS cc_start: 0.8769 (m90) cc_final: 0.8167 (m170) REVERT: K 73 GLU cc_start: 0.8312 (tt0) cc_final: 0.7697 (tt0) REVERT: K 77 ASP cc_start: 0.9318 (t70) cc_final: 0.9051 (t0) REVERT: K 80 THR cc_start: 0.8410 (p) cc_final: 0.7592 (p) REVERT: K 81 ASP cc_start: 0.8321 (m-30) cc_final: 0.8053 (m-30) REVERT: K 84 PHE cc_start: 0.8661 (m-80) cc_final: 0.8377 (m-80) REVERT: K 85 GLN cc_start: 0.9203 (mp10) cc_final: 0.8953 (mm110) REVERT: K 93 GLN cc_start: 0.8864 (pp30) cc_final: 0.8661 (pp30) REVERT: K 105 GLU cc_start: 0.9457 (tt0) cc_final: 0.9000 (pp20) REVERT: K 117 VAL cc_start: 0.9321 (m) cc_final: 0.8959 (p) REVERT: L 22 LEU cc_start: 0.8343 (mm) cc_final: 0.7797 (mm) REVERT: L 25 ASN cc_start: 0.8583 (m-40) cc_final: 0.7801 (m110) REVERT: L 45 ARG cc_start: 0.9274 (tpp80) cc_final: 0.8397 (tpp80) REVERT: L 82 THR cc_start: 0.9267 (p) cc_final: 0.8622 (p) REVERT: L 84 MET cc_start: 0.8772 (mpp) cc_final: 0.8290 (mpp) REVERT: L 88 TYR cc_start: 0.8758 (m-10) cc_final: 0.8312 (m-80) REVERT: M 57 TYR cc_start: 0.9358 (t80) cc_final: 0.8485 (t80) REVERT: M 72 ASP cc_start: 0.8525 (m-30) cc_final: 0.7950 (t70) REVERT: M 87 VAL cc_start: 0.9327 (t) cc_final: 0.9126 (t) REVERT: N 30 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7603 (ttm170) REVERT: N 39 TYR cc_start: 0.7882 (t80) cc_final: 0.7630 (t80) REVERT: N 68 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8409 (mm-30) REVERT: N 81 ASN cc_start: 0.8916 (t0) cc_final: 0.8460 (t0) REVERT: N 92 GLN cc_start: 0.9274 (tt0) cc_final: 0.8523 (tm-30) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1232 time to fit residues: 68.9527 Evaluate side-chains 301 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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: 20.0000 chunk 175 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN L 27 GLN ** M 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.111641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070912 restraints weight = 88589.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073203 restraints weight = 43501.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074557 restraints weight = 27007.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075297 restraints weight = 19910.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.075731 restraints weight = 16687.336| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20565 Z= 0.174 Angle : 0.729 10.567 29072 Z= 0.403 Chirality : 0.049 0.359 3279 Planarity : 0.006 0.112 2665 Dihedral : 29.652 176.619 5081 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.19), residues: 1699 helix: 0.65 (0.20), residues: 588 sheet: -0.95 (0.26), residues: 360 loop : -1.43 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 95 TYR 0.025 0.002 TYR H 98 PHE 0.023 0.002 PHE G 67 TRP 0.024 0.002 TRP D 327 HIS 0.009 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (20565) covalent geometry : angle 0.72949 / 0.40 (29072) hydrogen bonds : bond 0.08253 / 5.78 ( 1048) hydrogen bonds : angle 4.76408 / 3.28 ( 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 347 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.587 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: A 61 ILE cc_start: 0.1117 (mm) cc_final: 0.0640 (pt) REVERT: A 80 LYS cc_start: 0.1226 (mmtt) cc_final: 0.0724 (mtmt) REVERT: A 213 PHE cc_start: 0.5106 (p90) cc_final: 0.4411 (p90) REVERT: C 3931 MET cc_start: -0.1541 (mtt) cc_final: -0.2305 (ttt) REVERT: D 336 MET cc_start: 0.4993 (tmm) cc_final: 0.3401 (mmt) REVERT: G 51 ILE cc_start: 0.9364 (mt) cc_final: 0.9098 (mm) REVERT: G 55 GLN cc_start: 0.8896 (mt0) cc_final: 0.8233 (mt0) REVERT: G 58 THR cc_start: 0.9416 (p) cc_final: 0.9095 (p) REVERT: G 65 LEU cc_start: 0.9487 (mt) cc_final: 0.9181 (mm) REVERT: G 93 GLN cc_start: 0.8713 (pp30) cc_final: 0.6898 (tm-30) REVERT: G 97 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8297 (mt-10) REVERT: G 104 PHE cc_start: 0.9493 (m-80) cc_final: 0.9260 (m-80) REVERT: G 120 MET cc_start: 0.8724 (tpt) cc_final: 0.8190 (mmm) REVERT: G 133 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7325 (mp0) REVERT: H 25 ASN cc_start: 0.7954 (m-40) cc_final: 0.7719 (m-40) REVERT: H 27 GLN cc_start: 0.8918 (pp30) cc_final: 0.8634 (pp30) REVERT: H 29 ILE cc_start: 0.9347 (mm) cc_final: 0.9139 (pt) REVERT: H 63 GLU cc_start: 0.8912 (tp30) cc_final: 0.8619 (tp30) REVERT: H 73 THR cc_start: 0.9720 (m) cc_final: 0.9474 (p) REVERT: H 74 GLU cc_start: 0.8118 (tp30) cc_final: 0.7563 (tp30) REVERT: I 38 ASN cc_start: 0.9314 (m110) cc_final: 0.9058 (m110) REVERT: I 61 GLU cc_start: 0.8569 (mp0) cc_final: 0.8148 (mp0) REVERT: I 64 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8672 (tm-30) REVERT: I 79 ILE cc_start: 0.9619 (tp) cc_final: 0.9254 (tp) REVERT: I 90 ASP cc_start: 0.8734 (t0) cc_final: 0.8405 (t70) REVERT: I 104 GLN cc_start: 0.8915 (mp10) cc_final: 0.8294 (mp10) REVERT: J 57 SER cc_start: 0.9424 (m) cc_final: 0.9177 (p) REVERT: J 65 ASP cc_start: 0.9232 (t0) cc_final: 0.8970 (t0) REVERT: J 68 GLU cc_start: 0.8900 (tt0) cc_final: 0.8683 (tt0) REVERT: J 81 ASN cc_start: 0.9338 (t0) cc_final: 0.8881 (t0) REVERT: J 96 ARG cc_start: 0.9149 (mtp180) cc_final: 0.8762 (ttm110) REVERT: J 106 HIS cc_start: 0.8636 (m90) cc_final: 0.8099 (m170) REVERT: K 54 TYR cc_start: 0.8898 (m-10) cc_final: 0.8486 (m-10) REVERT: K 73 GLU cc_start: 0.8291 (tt0) cc_final: 0.7632 (tt0) REVERT: K 77 ASP cc_start: 0.9294 (t70) cc_final: 0.8985 (t0) REVERT: K 82 LEU cc_start: 0.8857 (mp) cc_final: 0.8610 (mp) REVERT: K 84 PHE cc_start: 0.8701 (m-80) cc_final: 0.8334 (m-80) REVERT: K 99 TYR cc_start: 0.8599 (t80) cc_final: 0.8261 (t80) REVERT: K 105 GLU cc_start: 0.9410 (tt0) cc_final: 0.8983 (pp20) REVERT: K 117 VAL cc_start: 0.9301 (m) cc_final: 0.8944 (p) REVERT: L 22 LEU cc_start: 0.8352 (mm) cc_final: 0.7822 (mm) REVERT: L 25 ASN cc_start: 0.8575 (m-40) cc_final: 0.7793 (m110) REVERT: L 45 ARG cc_start: 0.9277 (tpp80) cc_final: 0.8406 (tpp80) REVERT: L 82 THR cc_start: 0.9340 (p) cc_final: 0.8602 (p) REVERT: L 84 MET cc_start: 0.8694 (mpp) cc_final: 0.8205 (mpp) REVERT: L 88 TYR cc_start: 0.8784 (m-10) cc_final: 0.8365 (m-80) REVERT: L 98 TYR cc_start: 0.8132 (m-80) cc_final: 0.7543 (m-80) REVERT: M 57 TYR cc_start: 0.9327 (t80) cc_final: 0.8372 (t80) REVERT: M 68 ASN cc_start: 0.8731 (m110) cc_final: 0.8477 (m110) REVERT: M 72 ASP cc_start: 0.8569 (m-30) cc_final: 0.7959 (t70) REVERT: M 87 VAL cc_start: 0.9345 (t) cc_final: 0.9089 (t) REVERT: M 99 ARG cc_start: 0.8243 (mmt180) cc_final: 0.7628 (tpt170) REVERT: M 108 LEU cc_start: 0.9534 (pt) cc_final: 0.9158 (pt) REVERT: N 30 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7597 (ttm170) REVERT: N 38 VAL cc_start: 0.9757 (t) cc_final: 0.9430 (t) REVERT: N 59 MET cc_start: 0.9436 (mmm) cc_final: 0.9124 (mmm) REVERT: N 68 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8323 (mm-30) REVERT: N 81 ASN cc_start: 0.9218 (t0) cc_final: 0.8789 (t0) REVERT: N 92 GLN cc_start: 0.9274 (tt0) cc_final: 0.8567 (tm-30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1219 time to fit residues: 68.8206 Evaluate side-chains 309 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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: 10.0000 chunk 65 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 chunk 163 optimal weight: 0.3980 chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 G 108 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN M 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.111642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070892 restraints weight = 89136.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073109 restraints weight = 43834.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074446 restraints weight = 27307.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075303 restraints weight = 20072.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.075735 restraints weight = 16679.825| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20565 Z= 0.175 Angle : 0.728 10.397 29072 Z= 0.403 Chirality : 0.049 0.352 3279 Planarity : 0.005 0.070 2665 Dihedral : 29.567 176.269 5081 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.21 % Allowed : 0.14 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1699 helix: 0.72 (0.20), residues: 588 sheet: -0.90 (0.26), residues: 362 loop : -1.44 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 63 TYR 0.022 0.002 TYR H 98 PHE 0.028 0.002 PHE I 25 TRP 0.030 0.002 TRP D 327 HIS 0.008 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (20565) covalent geometry : angle 0.72839 / 0.40 (29072) hydrogen bonds : bond 0.08203 / 5.74 ( 1048) hydrogen bonds : angle 4.68546 / 3.23 ( 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 346 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 343 time to evaluate : 0.586 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: 0.1019 (mm) cc_final: 0.0544 (pt) REVERT: A 80 LYS cc_start: 0.1282 (mmtt) cc_final: 0.0716 (mtmt) REVERT: A 213 PHE cc_start: 0.5189 (p90) cc_final: 0.4518 (p90) REVERT: C 3931 MET cc_start: -0.1536 (mtt) cc_final: -0.2331 (ttt) REVERT: D 336 MET cc_start: 0.4987 (tmm) cc_final: 0.3520 (mmt) REVERT: G 51 ILE cc_start: 0.9343 (mt) cc_final: 0.9140 (mm) REVERT: G 55 GLN cc_start: 0.8960 (mt0) cc_final: 0.8517 (mt0) REVERT: G 61 LEU cc_start: 0.9112 (mm) cc_final: 0.8870 (mm) REVERT: G 93 GLN cc_start: 0.8552 (pp30) cc_final: 0.6719 (tm-30) REVERT: G 97 GLU cc_start: 0.8844 (mt-10) cc_final: 0.7771 (mt-10) REVERT: G 119 ILE cc_start: 0.8708 (pt) cc_final: 0.7412 (pt) REVERT: G 120 MET cc_start: 0.8696 (tpt) cc_final: 0.8122 (mmm) REVERT: G 133 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7314 (mp0) REVERT: H 27 GLN cc_start: 0.8927 (pp30) cc_final: 0.8668 (pp30) REVERT: H 29 ILE cc_start: 0.9358 (mm) cc_final: 0.9150 (pt) REVERT: H 63 GLU cc_start: 0.8953 (tp30) cc_final: 0.8654 (tp30) REVERT: H 73 THR cc_start: 0.9732 (m) cc_final: 0.9490 (p) REVERT: I 38 ASN cc_start: 0.9293 (m110) cc_final: 0.9076 (m110) REVERT: I 61 GLU cc_start: 0.8626 (mp0) cc_final: 0.8212 (mp0) REVERT: I 64 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8667 (tm-30) REVERT: I 90 ASP cc_start: 0.8745 (t0) cc_final: 0.8401 (t70) REVERT: I 104 GLN cc_start: 0.8924 (mp10) cc_final: 0.8344 (mp10) REVERT: J 57 SER cc_start: 0.9422 (m) cc_final: 0.9189 (p) REVERT: J 68 GLU cc_start: 0.8887 (tt0) cc_final: 0.8547 (tt0) REVERT: J 81 ASN cc_start: 0.9316 (t0) cc_final: 0.8767 (t0) REVERT: J 83 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8657 (mtp-110) REVERT: J 96 ARG cc_start: 0.9182 (mtp180) cc_final: 0.8769 (ttm110) REVERT: J 103 LEU cc_start: 0.9377 (mp) cc_final: 0.8984 (mp) REVERT: K 50 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8309 (tm-30) REVERT: K 51 ILE cc_start: 0.9261 (mt) cc_final: 0.8867 (mt) REVERT: K 64 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8672 (mmmm) REVERT: K 77 ASP cc_start: 0.9320 (t70) cc_final: 0.9069 (t0) REVERT: K 82 LEU cc_start: 0.8813 (mp) cc_final: 0.8551 (mp) REVERT: K 84 PHE cc_start: 0.8697 (m-80) cc_final: 0.8377 (m-80) REVERT: K 99 TYR cc_start: 0.8580 (t80) cc_final: 0.8327 (t80) REVERT: K 105 GLU cc_start: 0.9396 (tt0) cc_final: 0.8944 (pp20) REVERT: K 117 VAL cc_start: 0.9306 (m) cc_final: 0.8948 (p) REVERT: L 45 ARG cc_start: 0.9261 (tpp80) cc_final: 0.8441 (tpp80) REVERT: L 82 THR cc_start: 0.9323 (p) cc_final: 0.8647 (p) REVERT: L 84 MET cc_start: 0.8618 (mpp) cc_final: 0.8102 (mpp) REVERT: L 88 TYR cc_start: 0.8791 (m-10) cc_final: 0.8321 (m-80) REVERT: M 57 TYR cc_start: 0.9360 (t80) cc_final: 0.8417 (t80) REVERT: M 64 GLU cc_start: 0.9013 (pp20) cc_final: 0.8688 (pp20) REVERT: M 72 ASP cc_start: 0.8555 (m-30) cc_final: 0.7996 (t70) REVERT: M 87 VAL cc_start: 0.9333 (t) cc_final: 0.9063 (t) REVERT: M 92 GLU cc_start: 0.8968 (tt0) cc_final: 0.8653 (tt0) REVERT: M 99 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7681 (tpt170) REVERT: M 108 LEU cc_start: 0.9555 (pt) cc_final: 0.9258 (pt) REVERT: N 30 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7641 (ttm170) REVERT: N 39 TYR cc_start: 0.7900 (t80) cc_final: 0.7647 (t80) REVERT: N 59 MET cc_start: 0.9416 (mmm) cc_final: 0.9191 (mmp) REVERT: N 68 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8334 (mm-30) REVERT: N 81 ASN cc_start: 0.9066 (t0) cc_final: 0.8618 (t0) REVERT: N 92 GLN cc_start: 0.9285 (tt0) cc_final: 0.8549 (tm-30) outliers start: 3 outliers final: 1 residues processed: 344 average time/residue: 0.1172 time to fit residues: 65.5066 Evaluate side-chains 299 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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: 0.8980 chunk 152 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 40 optimal weight: 0.0570 chunk 50 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS K 68 GLN L 27 GLN M 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.113892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072294 restraints weight = 89046.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074522 restraints weight = 44062.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.075868 restraints weight = 27653.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076722 restraints weight = 20406.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077226 restraints weight = 16998.592| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20565 Z= 0.149 Angle : 0.713 9.752 29072 Z= 0.392 Chirality : 0.048 0.355 3279 Planarity : 0.005 0.068 2665 Dihedral : 29.445 177.361 5081 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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 are not related in a simple way. whole: -0.81 (0.20), residues: 1699 helix: 0.79 (0.21), residues: 588 sheet: -0.93 (0.27), residues: 361 loop : -1.37 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 95 TYR 0.025 0.002 TYR N 37 PHE 0.029 0.002 PHE I 25 TRP 0.028 0.002 TRP D 327 HIS 0.007 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (20565) covalent geometry : angle 0.71341 / 0.39 (29072) hydrogen bonds : bond 0.07942 / 5.63 ( 1048) hydrogen bonds : angle 4.55676 / 3.13 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4816.37 seconds wall clock time: 83 minutes 25.76 seconds (5005.76 seconds total)