Starting phenix.real_space_refine on Fri Sep 11 22:36:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9b_10735/09_2026/6y9b_10735.map" } resolution = 2.97 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 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: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 3 5.49 5 S 42 5.16 5 C 7851 2.51 5 N 1887 2.21 5 O 2103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 11889 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2019 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 13, 'TRANS': 230} Chain breaks: 1 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 977 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'HEM': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: A, B, M, N, I, J Time building chain proxies: 2.41, per 1000 atoms: 0.20 Number of scatterers: 11889 At special positions: 0 Unit cell: (104.907, 101.821, 114.163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 42 16.00 P 3 15.00 O 2103 8.00 N 1887 7.00 C 7851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 415.4 milliseconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 46.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 71 through 94 Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.514A pdb=" N ILE C 109 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 144 Proline residue: C 119 - end of helix removed outlier: 4.064A pdb=" N TYR C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Proline residue: C 132 - end of helix removed outlier: 3.653A pdb=" N ALA C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.802A pdb=" N THR C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 181 removed outlier: 3.585A pdb=" N LEU C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.641A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 236 removed outlier: 3.511A pdb=" N LEU C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 246 through 273 removed outlier: 3.504A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.759A pdb=" N ILE C 293 " --> pdb=" O PRO C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.832A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.696A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.695A pdb=" N THR I 91 " --> pdb=" O THR I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS J 65 " --> pdb=" O PRO J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.696A pdb=" N THR J 91 " --> pdb=" O THR J 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 89 removed outlier: 3.832A pdb=" N LEU M 89 " --> pdb=" O ALA M 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 89 removed outlier: 3.832A pdb=" N LEU N 89 " --> pdb=" O ALA N 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 71 through 94 Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.516A pdb=" N ILE A 109 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 144 Proline residue: A 119 - end of helix removed outlier: 4.064A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Proline residue: A 132 - end of helix removed outlier: 3.653A pdb=" N ALA A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.802A pdb=" N THR A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 removed outlier: 3.584A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.641A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 236 removed outlier: 3.512A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 246 through 273 removed outlier: 3.504A pdb=" N LEU A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.759A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 71 through 94 Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.516A pdb=" N ILE B 109 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 144 Proline residue: B 119 - end of helix removed outlier: 4.063A pdb=" N TYR B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Proline residue: B 132 - end of helix removed outlier: 3.652A pdb=" N ALA B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.803A pdb=" N THR B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 181 removed outlier: 3.585A pdb=" N LEU B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.640A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 236 removed outlier: 3.512A pdb=" N LEU B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 246 through 273 removed outlier: 3.503A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.760A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.020A pdb=" N ASP L 76 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.617A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.822A pdb=" N THR L 103 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.571A pdb=" N TYR L 31 " --> pdb=" O LYS L 36 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA6, first strand: chain 'H' and resid 18 through 21 removed outlier: 3.739A pdb=" N LEU H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.099A pdb=" N LEU H 46 " --> pdb=" O PHE H 41 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE H 41 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AA9, first strand: chain 'I' and resid 18 through 21 removed outlier: 3.739A pdb=" N LEU I 83 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.099A pdb=" N LEU I 46 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE I 41 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG I 39 " --> pdb=" O TRP I 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AB3, first strand: chain 'J' and resid 18 through 21 removed outlier: 3.739A pdb=" N LEU J 83 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.099A pdb=" N LEU J 46 " --> pdb=" O PHE J 41 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE J 41 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG J 39 " --> pdb=" O TRP J 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 5 through 6 removed outlier: 4.021A pdb=" N ASP M 76 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.617A pdb=" N LEU M 39 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR M 55 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.822A pdb=" N THR M 103 " --> pdb=" O GLN M 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.572A pdb=" N TYR M 31 " --> pdb=" O LYS M 36 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS M 36 " --> pdb=" O TYR M 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 6 removed outlier: 4.021A pdb=" N ASP N 76 " --> pdb=" O SER N 73 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.617A pdb=" N LEU N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR N 55 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.822A pdb=" N THR N 103 " --> pdb=" O GLN N 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 30 through 31 removed outlier: 3.571A pdb=" N TYR N 31 " --> pdb=" O LYS N 36 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS N 36 " --> pdb=" O TYR N 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 609 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 4690 1.38 - 1.56: 7472 1.56 - 1.74: 3 1.74 - 1.92: 72 1.92 - 2.10: 9 Bond restraints: 12246 Sorted by residual: bond pdb=" O4 XP4 A 402 " pdb=" P1 XP4 A 402 " ideal model delta sigma weight residual 1.708 1.613 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O4 XP4 B 402 " pdb=" P1 XP4 B 402 " ideal model delta sigma weight residual 1.708 1.613 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O4 XP4 C 402 " pdb=" P1 XP4 C 402 " ideal model delta sigma weight residual 1.708 1.614 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C3C HEM B 401 " pdb=" CAC HEM B 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C3C HEM A 401 " pdb=" CAC HEM A 401 " ideal model delta sigma weight residual 1.544 1.469 0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 12241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 16133 1.29 - 2.58: 392 2.58 - 3.87: 109 3.87 - 5.16: 48 5.16 - 6.45: 19 Bond angle restraints: 16701 Sorted by residual: angle pdb=" C2D HEM A 401 " pdb=" C1D HEM A 401 " pdb=" CHD HEM A 401 " ideal model delta sigma weight residual 126.00 120.71 5.29 3.00e+00 1.11e-01 3.11e+00 angle pdb=" C2D HEM C 401 " pdb=" C1D HEM C 401 " pdb=" CHD HEM C 401 " ideal model delta sigma weight residual 126.00 120.74 5.26 3.00e+00 1.11e-01 3.07e+00 angle pdb=" C2D HEM B 401 " pdb=" C1D HEM B 401 " pdb=" CHD HEM B 401 " ideal model delta sigma weight residual 126.00 120.75 5.25 3.00e+00 1.11e-01 3.07e+00 angle pdb=" C1A HEM A 401 " pdb=" CHA HEM A 401 " pdb=" C4D HEM A 401 " ideal model delta sigma weight residual 126.00 120.75 5.25 3.00e+00 1.11e-01 3.06e+00 angle pdb=" C2B HEM A 401 " pdb=" C1B HEM A 401 " pdb=" CHB HEM A 401 " ideal model delta sigma weight residual 126.00 120.75 5.25 3.00e+00 1.11e-01 3.06e+00 ... (remaining 16696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6781 17.66 - 35.32: 227 35.32 - 52.98: 48 52.98 - 70.64: 18 70.64 - 88.30: 15 Dihedral angle restraints: 7089 sinusoidal: 2844 harmonic: 4245 Sorted by residual: dihedral pdb=" C2C HEM B 401 " pdb=" C3C HEM B 401 " pdb=" CAC HEM B 401 " pdb=" CBC HEM B 401 " ideal model delta sinusoidal sigma weight residual 0.00 -71.90 71.90 2 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2C HEM C 401 " pdb=" C3C HEM C 401 " pdb=" CAC HEM C 401 " pdb=" CBC HEM C 401 " ideal model delta sinusoidal sigma weight residual 0.00 -71.88 71.88 2 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2C HEM A 401 " pdb=" C3C HEM A 401 " pdb=" CAC HEM A 401 " pdb=" CBC HEM A 401 " ideal model delta sinusoidal sigma weight residual 0.00 -71.77 71.77 2 1.00e+01 1.00e-02 4.33e+01 ... (remaining 7086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1073 0.026 - 0.053: 473 0.053 - 0.079: 170 0.079 - 0.105: 84 0.105 - 0.132: 33 Chirality restraints: 1833 Sorted by residual: chirality pdb=" CA ILE B 238 " pdb=" N ILE B 238 " pdb=" C ILE B 238 " pdb=" CB ILE B 238 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE C 238 " pdb=" N ILE C 238 " pdb=" C ILE C 238 " pdb=" CB ILE C 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1830 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 XP4 C 402 " -0.022 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C19 XP4 C 402 " 0.006 2.00e-02 2.50e+03 pdb=" O7 XP4 C 402 " 0.007 2.00e-02 2.50e+03 pdb=" O8 XP4 C 402 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM B 401 " 0.010 2.00e-02 2.50e+03 8.54e-03 1.64e+00 pdb=" C2A HEM B 401 " 0.005 2.00e-02 2.50e+03 pdb=" C3A HEM B 401 " -0.001 2.00e-02 2.50e+03 pdb=" C4A HEM B 401 " 0.006 2.00e-02 2.50e+03 pdb=" CAA HEM B 401 " -0.008 2.00e-02 2.50e+03 pdb=" CHA HEM B 401 " 0.005 2.00e-02 2.50e+03 pdb=" CHB HEM B 401 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM B 401 " 0.000 2.00e-02 2.50e+03 pdb=" NA HEM B 401 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 401 " -0.009 2.00e-02 2.50e+03 8.54e-03 1.64e+00 pdb=" C2A HEM C 401 " -0.006 2.00e-02 2.50e+03 pdb=" C3A HEM C 401 " 0.000 2.00e-02 2.50e+03 pdb=" C4A HEM C 401 " -0.006 2.00e-02 2.50e+03 pdb=" CAA HEM C 401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA HEM C 401 " -0.005 2.00e-02 2.50e+03 pdb=" CHB HEM C 401 " -0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 401 " 0.000 2.00e-02 2.50e+03 pdb=" NA HEM C 401 " 0.020 2.00e-02 2.50e+03 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 87 2.57 - 3.15: 9834 3.15 - 3.74: 17868 3.74 - 4.32: 26352 4.32 - 4.90: 45146 Nonbonded interactions: 99287 Sorted by model distance: nonbonded pdb=" NE2 HIS C 268 " pdb="FE HEM C 401 " model vdw 1.990 3.080 nonbonded pdb=" NE2 HIS B 268 " pdb="FE HEM B 401 " model vdw 1.991 3.080 nonbonded pdb=" NE2 HIS A 268 " pdb="FE HEM A 401 " model vdw 1.991 3.080 nonbonded pdb=" OH TYR A 88 " pdb=" O PRO A 288 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR C 88 " pdb=" O PRO C 288 " model vdw 2.232 3.040 ... (remaining 99282 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.007 0.217 12255 Z= 0.267 Angle : 0.585 6.446 16713 Z= 0.279 Chirality : 0.039 0.132 1833 Planarity : 0.003 0.026 2004 Dihedral : 10.923 88.295 4347 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.17 % Allowed : 5.37 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.00 (0.18), residues: 1410 helix: -2.56 (0.15), residues: 597 sheet: -2.91 (0.23), residues: 315 loop : -2.17 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.016 0.001 TYR B 219 PHE 0.007 0.001 PHE B 291 TRP 0.009 0.001 TRP A 285 HIS 0.001 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.27 (12246) covalent geometry : angle 0.58498 / 0.28 (16701) SS BOND : bond 0.00237 / 0.12 ( 6) SS BOND : angle 1.05105 / 0.48 ( 12) hydrogen bonds : bond 0.25877 / 17.32 ( 594) hydrogen bonds : angle 8.83507 / 6.44 ( 1683) Misc. bond : bond 0.17803 / 8.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7818 (mp0) REVERT: C 143 ASN cc_start: 0.8173 (m110) cc_final: 0.7892 (p0) REVERT: C 158 MET cc_start: 0.8607 (mmm) cc_final: 0.8387 (mmm) REVERT: C 274 TRP cc_start: 0.7875 (t-100) cc_final: 0.7177 (t-100) REVERT: C 279 ASP cc_start: 0.8757 (t0) cc_final: 0.8304 (t0) REVERT: L 85 LYS cc_start: 0.9020 (mttt) cc_final: 0.8764 (mmmm) REVERT: H 3 GLN cc_start: 0.8012 (tp40) cc_final: 0.7600 (tm-30) REVERT: H 5 GLN cc_start: 0.8623 (tt0) cc_final: 0.8155 (pp30) REVERT: H 13 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8424 (mmmt) REVERT: H 47 GLU cc_start: 0.8544 (tt0) cc_final: 0.8195 (tt0) REVERT: H 73 ASP cc_start: 0.8596 (t0) cc_final: 0.8376 (t0) REVERT: H 100 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8108 (mtp85) REVERT: H 103 ASP cc_start: 0.8263 (t0) cc_final: 0.7879 (t70) REVERT: H 105 ASP cc_start: 0.8208 (m-30) cc_final: 0.7911 (m-30) REVERT: I 3 GLN cc_start: 0.8190 (tp40) cc_final: 0.7781 (tm-30) REVERT: I 5 GLN cc_start: 0.8584 (tt0) cc_final: 0.8171 (pp30) REVERT: I 13 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8512 (mmmt) REVERT: I 44 ASN cc_start: 0.8557 (m110) cc_final: 0.7873 (p0) REVERT: I 45 LYS cc_start: 0.8472 (tttt) cc_final: 0.8207 (tttp) REVERT: I 73 ASP cc_start: 0.8467 (t0) cc_final: 0.7968 (t0) REVERT: I 103 ASP cc_start: 0.8106 (t0) cc_final: 0.7496 (t0) REVERT: I 105 ASP cc_start: 0.8403 (m-30) cc_final: 0.8198 (m-30) REVERT: J 3 GLN cc_start: 0.8071 (tp40) cc_final: 0.7660 (tm-30) REVERT: J 5 GLN cc_start: 0.8566 (tt0) cc_final: 0.8085 (pp30) REVERT: J 22 CYS cc_start: 0.6565 (t) cc_final: 0.6308 (t) REVERT: J 73 ASP cc_start: 0.8730 (t0) cc_final: 0.8218 (t0) REVERT: J 78 GLN cc_start: 0.9004 (mt0) cc_final: 0.8770 (mt0) REVERT: J 87 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8457 (t) REVERT: J 103 ASP cc_start: 0.8165 (t0) cc_final: 0.7688 (t70) REVERT: J 105 ASP cc_start: 0.8201 (m-30) cc_final: 0.7932 (m-30) REVERT: M 55 TYR cc_start: 0.8787 (p90) cc_final: 0.8494 (p90) REVERT: M 85 LYS cc_start: 0.9015 (mttt) cc_final: 0.8382 (mtpm) REVERT: M 87 GLU cc_start: 0.8526 (pm20) cc_final: 0.7550 (pm20) REVERT: M 88 ASP cc_start: 0.8651 (m-30) cc_final: 0.8396 (m-30) REVERT: N 85 LYS cc_start: 0.8830 (mttt) cc_final: 0.8500 (mtmt) REVERT: N 87 GLU cc_start: 0.8711 (pm20) cc_final: 0.8465 (pm20) REVERT: N 111 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 93 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 143 ASN cc_start: 0.8357 (m110) cc_final: 0.8000 (p0) REVERT: A 212 ASP cc_start: 0.8648 (t0) cc_final: 0.8111 (t0) REVERT: A 274 TRP cc_start: 0.7829 (t-100) cc_final: 0.7298 (t-100) REVERT: A 279 ASP cc_start: 0.8940 (t0) cc_final: 0.8514 (t0) REVERT: B 93 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7804 (mp0) REVERT: B 143 ASN cc_start: 0.8225 (m110) cc_final: 0.7999 (p0) REVERT: B 243 ASP cc_start: 0.8112 (m-30) cc_final: 0.7870 (m-30) REVERT: B 274 TRP cc_start: 0.7925 (t-100) cc_final: 0.7328 (t-100) REVERT: B 279 ASP cc_start: 0.8957 (t0) cc_final: 0.8542 (t0) REVERT: B 292 MET cc_start: 0.8502 (mtp) cc_final: 0.8217 (mtt) outliers start: 15 outliers final: 4 residues processed: 272 average time/residue: 0.6617 time to fit residues: 192.3264 Evaluate side-chains 194 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 96 HIS C 202 GLN C 254 GLN L 6 GLN L 37 ASN H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 37 ASN N 6 GLN N 37 ASN A 96 HIS ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN B 96 HIS B 202 GLN B 254 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.056250 restraints weight = 25866.895| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.54 r_work: 0.2658 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.296 12255 Z= 0.139 Angle : 0.618 9.573 16713 Z= 0.304 Chirality : 0.041 0.173 1833 Planarity : 0.004 0.035 2004 Dihedral : 8.432 85.588 1683 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.26 % Allowed : 12.38 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.32 (0.21), residues: 1410 helix: 0.31 (0.20), residues: 630 sheet: -2.07 (0.24), residues: 318 loop : -1.42 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 215 TYR 0.027 0.001 TYR A 219 PHE 0.010 0.001 PHE B 291 TRP 0.008 0.001 TRP B 214 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (12246) covalent geometry : angle 0.61816 / 0.30 (16701) SS BOND : bond 0.00329 / 0.17 ( 6) SS BOND : angle 0.80636 / 0.37 ( 12) hydrogen bonds : bond 0.05179 / 3.42 ( 594) hydrogen bonds : angle 4.83379 / 3.48 ( 1683) Misc. bond : bond 0.29079 / 14.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8019 (mp0) REVERT: C 120 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8027 (tpp) REVERT: C 158 MET cc_start: 0.8651 (mmm) cc_final: 0.8342 (tpp) REVERT: C 274 TRP cc_start: 0.7885 (t-100) cc_final: 0.7097 (t-100) REVERT: C 279 ASP cc_start: 0.8793 (t0) cc_final: 0.8246 (t0) REVERT: C 292 MET cc_start: 0.8915 (mtm) cc_final: 0.8709 (mtt) REVERT: L 17 GLU cc_start: 0.8596 (tt0) cc_final: 0.8044 (tt0) REVERT: L 32 ARG cc_start: 0.8571 (mtm180) cc_final: 0.8322 (mtm-85) REVERT: L 35 GLN cc_start: 0.8844 (mt0) cc_final: 0.8554 (mt0) REVERT: L 87 GLU cc_start: 0.8647 (pm20) cc_final: 0.8399 (pm20) REVERT: H 3 GLN cc_start: 0.8169 (tp40) cc_final: 0.7395 (tm-30) REVERT: H 5 GLN cc_start: 0.8848 (tt0) cc_final: 0.8046 (pp30) REVERT: H 13 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8432 (mmmt) REVERT: H 45 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8372 (tttp) REVERT: H 47 GLU cc_start: 0.9080 (tt0) cc_final: 0.8793 (tt0) REVERT: H 73 ASP cc_start: 0.7928 (t0) cc_final: 0.7292 (t0) REVERT: H 81 LEU cc_start: 0.8860 (tp) cc_final: 0.8577 (tm) REVERT: H 82 GLN cc_start: 0.7677 (mp10) cc_final: 0.7252 (mp10) REVERT: H 89 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8869 (mp0) REVERT: H 100 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8125 (mtp85) REVERT: H 103 ASP cc_start: 0.8383 (t0) cc_final: 0.7645 (t70) REVERT: H 105 ASP cc_start: 0.8588 (m-30) cc_final: 0.8154 (m-30) REVERT: I 3 GLN cc_start: 0.8283 (tp40) cc_final: 0.7775 (tm-30) REVERT: I 5 GLN cc_start: 0.8752 (tt0) cc_final: 0.8269 (tm-30) REVERT: I 44 ASN cc_start: 0.8791 (m110) cc_final: 0.7930 (p0) REVERT: I 45 LYS cc_start: 0.8478 (tttt) cc_final: 0.8223 (tttp) REVERT: I 73 ASP cc_start: 0.7846 (t0) cc_final: 0.7204 (t0) REVERT: I 103 ASP cc_start: 0.8222 (t0) cc_final: 0.7478 (t0) REVERT: I 105 ASP cc_start: 0.8791 (m-30) cc_final: 0.8425 (m-30) REVERT: J 3 GLN cc_start: 0.8174 (tp40) cc_final: 0.7772 (tp40) REVERT: J 5 GLN cc_start: 0.8836 (tt0) cc_final: 0.8025 (pp30) REVERT: J 47 GLU cc_start: 0.9067 (tt0) cc_final: 0.8785 (tt0) REVERT: J 73 ASP cc_start: 0.8122 (t0) cc_final: 0.7444 (t0) REVERT: J 78 GLN cc_start: 0.8637 (mt0) cc_final: 0.8426 (mt0) REVERT: J 82 GLN cc_start: 0.7601 (mp10) cc_final: 0.7075 (mp10) REVERT: J 87 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8034 (t) REVERT: J 89 GLU cc_start: 0.8803 (mp0) cc_final: 0.8321 (mp0) REVERT: J 100 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8352 (mmm-85) REVERT: J 103 ASP cc_start: 0.8301 (t0) cc_final: 0.7556 (t70) REVERT: J 105 ASP cc_start: 0.8590 (m-30) cc_final: 0.8176 (m-30) REVERT: M 32 ARG cc_start: 0.8471 (mtm180) cc_final: 0.8217 (mtm-85) REVERT: M 85 LYS cc_start: 0.8397 (mttt) cc_final: 0.7872 (mtpm) REVERT: M 87 GLU cc_start: 0.8694 (pm20) cc_final: 0.7758 (pm20) REVERT: M 88 ASP cc_start: 0.8371 (m-30) cc_final: 0.8143 (m-30) REVERT: N 17 GLU cc_start: 0.8480 (tt0) cc_final: 0.7796 (tt0) REVERT: N 60 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.8526 (ttm110) REVERT: N 85 LYS cc_start: 0.8094 (mttt) cc_final: 0.7714 (mtpp) REVERT: N 87 GLU cc_start: 0.8849 (pm20) cc_final: 0.8414 (pm20) REVERT: A 120 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8082 (tpp) REVERT: A 206 ASP cc_start: 0.8341 (t0) cc_final: 0.8111 (t0) REVERT: A 274 TRP cc_start: 0.7571 (t-100) cc_final: 0.7007 (t-100) REVERT: A 279 ASP cc_start: 0.8889 (t0) cc_final: 0.8394 (t0) REVERT: B 93 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8298 (mm-30) REVERT: B 158 MET cc_start: 0.8699 (mmm) cc_final: 0.8486 (mmm) REVERT: B 243 ASP cc_start: 0.8523 (m-30) cc_final: 0.8315 (m-30) REVERT: B 248 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8303 (tmm-80) REVERT: B 274 TRP cc_start: 0.8137 (t-100) cc_final: 0.7261 (t-100) REVERT: B 279 ASP cc_start: 0.8980 (t0) cc_final: 0.8453 (t0) REVERT: B 292 MET cc_start: 0.8806 (mtp) cc_final: 0.8491 (mtt) outliers start: 29 outliers final: 9 residues processed: 233 average time/residue: 0.6601 time to fit residues: 164.3726 Evaluate side-chains 205 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 120 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 ASN H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN J 36 ASN A 143 ASN A 202 GLN B 143 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.055979 restraints weight = 26133.007| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.57 r_work: 0.2640 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 12255 Z= 0.137 Angle : 0.606 12.175 16713 Z= 0.286 Chirality : 0.040 0.168 1833 Planarity : 0.004 0.030 2004 Dihedral : 7.962 77.788 1681 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.27 % Allowed : 12.93 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.26 (0.22), residues: 1410 helix: 1.33 (0.21), residues: 630 sheet: -1.58 (0.27), residues: 318 loop : -1.09 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 32 TYR 0.026 0.001 TYR C 219 PHE 0.009 0.001 PHE B 291 TRP 0.008 0.001 TRP C 274 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (12246) covalent geometry : angle 0.60571 / 0.29 (16701) SS BOND : bond 0.00272 / 0.14 ( 6) SS BOND : angle 1.02124 / 0.45 ( 12) hydrogen bonds : bond 0.04428 / 2.92 ( 594) hydrogen bonds : angle 4.30996 / 3.09 ( 1683) Misc. bond : bond 0.29453 / 14.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8242 (mm-30) REVERT: C 120 MET cc_start: 0.8618 (tpp) cc_final: 0.8411 (tpt) REVERT: C 158 MET cc_start: 0.8516 (mmm) cc_final: 0.8275 (tpp) REVERT: C 212 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8366 (t0) REVERT: C 274 TRP cc_start: 0.7962 (t-100) cc_final: 0.7185 (t-100) REVERT: C 292 MET cc_start: 0.8911 (mtm) cc_final: 0.8567 (mtt) REVERT: L 17 GLU cc_start: 0.8590 (tt0) cc_final: 0.8081 (tt0) REVERT: L 35 GLN cc_start: 0.8875 (mt0) cc_final: 0.8507 (mt0) REVERT: L 87 GLU cc_start: 0.8602 (pm20) cc_final: 0.8392 (pm20) REVERT: L 88 ASP cc_start: 0.8503 (m-30) cc_final: 0.8226 (m-30) REVERT: H 3 GLN cc_start: 0.8246 (tp40) cc_final: 0.7492 (tm-30) REVERT: H 5 GLN cc_start: 0.8732 (tt0) cc_final: 0.8012 (tm-30) REVERT: H 13 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8372 (mmmt) REVERT: H 45 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8386 (tttp) REVERT: H 47 GLU cc_start: 0.9091 (tt0) cc_final: 0.8825 (tt0) REVERT: H 67 ARG cc_start: 0.8608 (ptt90) cc_final: 0.8382 (ptm-80) REVERT: H 73 ASP cc_start: 0.8001 (t0) cc_final: 0.7408 (t0) REVERT: H 81 LEU cc_start: 0.8830 (tp) cc_final: 0.8551 (tm) REVERT: H 82 GLN cc_start: 0.7693 (mp10) cc_final: 0.7318 (mp10) REVERT: H 89 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8906 (mp0) REVERT: H 100 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8125 (mtp85) REVERT: H 103 ASP cc_start: 0.8353 (t0) cc_final: 0.7566 (t70) REVERT: H 105 ASP cc_start: 0.8619 (m-30) cc_final: 0.8157 (m-30) REVERT: I 3 GLN cc_start: 0.8360 (tp40) cc_final: 0.7824 (tm-30) REVERT: I 5 GLN cc_start: 0.8761 (tt0) cc_final: 0.8289 (tm-30) REVERT: I 27 TYR cc_start: 0.8308 (t80) cc_final: 0.8080 (t80) REVERT: I 44 ASN cc_start: 0.8799 (m110) cc_final: 0.7928 (p0) REVERT: I 45 LYS cc_start: 0.8530 (tttt) cc_final: 0.8261 (tttp) REVERT: I 73 ASP cc_start: 0.8034 (t0) cc_final: 0.7430 (t0) REVERT: I 90 ASP cc_start: 0.8262 (m-30) cc_final: 0.7634 (m-30) REVERT: I 100 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8241 (mmm-85) REVERT: I 103 ASP cc_start: 0.8278 (t0) cc_final: 0.7513 (t0) REVERT: I 105 ASP cc_start: 0.8796 (m-30) cc_final: 0.8424 (m-30) REVERT: J 3 GLN cc_start: 0.8263 (tp40) cc_final: 0.7854 (tp40) REVERT: J 5 GLN cc_start: 0.8885 (tt0) cc_final: 0.8122 (tm-30) REVERT: J 47 GLU cc_start: 0.9092 (tt0) cc_final: 0.8885 (tt0) REVERT: J 67 ARG cc_start: 0.8566 (ptt90) cc_final: 0.8211 (ptt90) REVERT: J 73 ASP cc_start: 0.8164 (t0) cc_final: 0.7515 (t0) REVERT: J 82 GLN cc_start: 0.7720 (mp10) cc_final: 0.7443 (mp10) REVERT: J 87 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.7867 (m) REVERT: J 90 ASP cc_start: 0.8350 (m-30) cc_final: 0.7296 (m-30) REVERT: J 100 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8354 (mmm-85) REVERT: J 103 ASP cc_start: 0.8341 (t0) cc_final: 0.7580 (t70) REVERT: J 105 ASP cc_start: 0.8611 (m-30) cc_final: 0.8151 (m-30) REVERT: M 17 GLU cc_start: 0.8731 (tt0) cc_final: 0.8491 (tt0) REVERT: M 32 ARG cc_start: 0.8455 (mtm180) cc_final: 0.8237 (mpp-170) REVERT: M 85 LYS cc_start: 0.8439 (mttt) cc_final: 0.7881 (mtpm) REVERT: M 87 GLU cc_start: 0.8734 (pm20) cc_final: 0.7780 (pm20) REVERT: M 88 ASP cc_start: 0.8444 (m-30) cc_final: 0.8159 (m-30) REVERT: N 17 GLU cc_start: 0.8508 (tt0) cc_final: 0.7860 (tt0) REVERT: N 60 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8659 (ttm110) REVERT: N 85 LYS cc_start: 0.8258 (mttt) cc_final: 0.7852 (mtpp) REVERT: N 87 GLU cc_start: 0.8890 (pm20) cc_final: 0.8463 (pm20) REVERT: N 110 LEU cc_start: 0.9142 (tp) cc_final: 0.8914 (tt) REVERT: A 93 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8497 (mm-30) REVERT: A 216 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8594 (tpp) REVERT: A 274 TRP cc_start: 0.7642 (t-100) cc_final: 0.7045 (t-100) REVERT: A 279 ASP cc_start: 0.8868 (t0) cc_final: 0.8372 (t0) REVERT: B 93 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 140 GLN cc_start: 0.8607 (tt0) cc_final: 0.8323 (tm130) REVERT: B 158 MET cc_start: 0.8704 (mmm) cc_final: 0.8228 (tpp) REVERT: B 201 GLN cc_start: 0.9065 (tp40) cc_final: 0.8756 (tp40) REVERT: B 243 ASP cc_start: 0.8643 (m-30) cc_final: 0.8423 (m-30) REVERT: B 274 TRP cc_start: 0.8218 (t-100) cc_final: 0.7385 (t-100) REVERT: B 279 ASP cc_start: 0.8991 (t0) cc_final: 0.8433 (t0) outliers start: 42 outliers final: 18 residues processed: 233 average time/residue: 0.6410 time to fit residues: 159.6530 Evaluate side-chains 210 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN J 16 GLN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054131 restraints weight = 26332.476| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.58 r_work: 0.2592 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.359 12255 Z= 0.212 Angle : 0.664 13.896 16713 Z= 0.310 Chirality : 0.042 0.167 1833 Planarity : 0.004 0.029 2004 Dihedral : 8.018 77.009 1681 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.12 % Allowed : 14.72 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.06 (0.23), residues: 1410 helix: 1.55 (0.21), residues: 630 sheet: -1.47 (0.27), residues: 324 loop : -0.81 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 248 TYR 0.027 0.002 TYR B 219 PHE 0.008 0.001 PHE C 291 TRP 0.011 0.001 TRP B 274 HIS 0.004 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (12246) covalent geometry : angle 0.66318 / 0.31 (16701) SS BOND : bond 0.00305 / 0.15 ( 6) SS BOND : angle 1.25058 / 0.57 ( 12) hydrogen bonds : bond 0.04676 / 3.09 ( 594) hydrogen bonds : angle 4.28660 / 3.07 ( 1683) Misc. bond : bond 0.35816 / 17.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8258 (mm-30) REVERT: C 158 MET cc_start: 0.8547 (mmm) cc_final: 0.8325 (tpp) REVERT: C 274 TRP cc_start: 0.8047 (t-100) cc_final: 0.7297 (t-100) REVERT: C 279 ASP cc_start: 0.8846 (t0) cc_final: 0.8276 (t0) REVERT: C 292 MET cc_start: 0.8983 (mtm) cc_final: 0.8636 (mtt) REVERT: L 17 GLU cc_start: 0.8565 (tt0) cc_final: 0.8060 (tt0) REVERT: L 35 GLN cc_start: 0.8937 (mt0) cc_final: 0.8624 (mt0) REVERT: L 87 GLU cc_start: 0.8632 (pm20) cc_final: 0.8398 (pm20) REVERT: L 88 ASP cc_start: 0.8647 (m-30) cc_final: 0.8363 (m-30) REVERT: H 3 GLN cc_start: 0.8382 (tp40) cc_final: 0.7734 (tm-30) REVERT: H 5 GLN cc_start: 0.8857 (tt0) cc_final: 0.7786 (pp30) REVERT: H 13 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8334 (mmmt) REVERT: H 45 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8451 (tttp) REVERT: H 47 GLU cc_start: 0.9074 (tt0) cc_final: 0.8752 (tt0) REVERT: H 73 ASP cc_start: 0.8201 (t0) cc_final: 0.7597 (t0) REVERT: H 82 GLN cc_start: 0.7883 (mp10) cc_final: 0.7482 (mp10) REVERT: H 89 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8951 (mp0) REVERT: H 100 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8224 (mtp85) REVERT: H 103 ASP cc_start: 0.8554 (t0) cc_final: 0.7812 (t70) REVERT: H 105 ASP cc_start: 0.8725 (m-30) cc_final: 0.8334 (m-30) REVERT: I 3 GLN cc_start: 0.8441 (tp40) cc_final: 0.7953 (tm-30) REVERT: I 5 GLN cc_start: 0.8802 (tt0) cc_final: 0.8232 (tm-30) REVERT: I 44 ASN cc_start: 0.8867 (m110) cc_final: 0.7987 (p0) REVERT: I 45 LYS cc_start: 0.8668 (tttt) cc_final: 0.8392 (tttp) REVERT: I 73 ASP cc_start: 0.8099 (t0) cc_final: 0.7597 (t0) REVERT: I 90 ASP cc_start: 0.8098 (m-30) cc_final: 0.7896 (m-30) REVERT: I 100 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8304 (mmm-85) REVERT: I 103 ASP cc_start: 0.8460 (t0) cc_final: 0.7734 (t0) REVERT: I 105 ASP cc_start: 0.8786 (m-30) cc_final: 0.8456 (m-30) REVERT: J 3 GLN cc_start: 0.8327 (tp40) cc_final: 0.7894 (tp40) REVERT: J 5 GLN cc_start: 0.8818 (tt0) cc_final: 0.8125 (tm-30) REVERT: J 67 ARG cc_start: 0.8659 (ptt90) cc_final: 0.8427 (ptt90) REVERT: J 73 ASP cc_start: 0.8208 (t0) cc_final: 0.7603 (t0) REVERT: J 87 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (t) REVERT: J 90 ASP cc_start: 0.8161 (m-30) cc_final: 0.7667 (m-30) REVERT: J 100 ARG cc_start: 0.8708 (mtp85) cc_final: 0.8481 (mmm-85) REVERT: J 103 ASP cc_start: 0.8544 (t0) cc_final: 0.7754 (t70) REVERT: J 105 ASP cc_start: 0.8664 (m-30) cc_final: 0.8272 (m-30) REVERT: M 17 GLU cc_start: 0.8610 (tt0) cc_final: 0.8394 (tt0) REVERT: M 61 GLU cc_start: 0.8619 (tp30) cc_final: 0.8390 (tp30) REVERT: M 85 LYS cc_start: 0.8546 (mttt) cc_final: 0.8060 (mtpt) REVERT: M 87 GLU cc_start: 0.8871 (pm20) cc_final: 0.8270 (pm20) REVERT: M 88 ASP cc_start: 0.8621 (m-30) cc_final: 0.8225 (m-30) REVERT: N 17 GLU cc_start: 0.8474 (tt0) cc_final: 0.7818 (tt0) REVERT: N 85 LYS cc_start: 0.8454 (mttt) cc_final: 0.8161 (mmmm) REVERT: N 87 GLU cc_start: 0.8932 (pm20) cc_final: 0.8612 (pm20) REVERT: A 104 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7346 (tp40) REVERT: A 274 TRP cc_start: 0.7931 (t-100) cc_final: 0.7170 (t-100) REVERT: A 279 ASP cc_start: 0.8912 (t0) cc_final: 0.8403 (t0) REVERT: B 93 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 158 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8360 (tpp) REVERT: B 243 ASP cc_start: 0.8655 (m-30) cc_final: 0.8444 (m-30) REVERT: B 274 TRP cc_start: 0.8221 (t-100) cc_final: 0.7453 (t-100) REVERT: B 279 ASP cc_start: 0.9028 (t0) cc_final: 0.8488 (t0) REVERT: B 292 MET cc_start: 0.8817 (mtp) cc_final: 0.8459 (mtt) outliers start: 40 outliers final: 21 residues processed: 228 average time/residue: 0.6657 time to fit residues: 162.5372 Evaluate side-chains 206 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 ASN I 54 ASN I 82 GLN J 36 ASN N 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.056094 restraints weight = 25927.961| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.54 r_work: 0.2648 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.269 12255 Z= 0.131 Angle : 0.597 10.815 16713 Z= 0.282 Chirality : 0.040 0.168 1833 Planarity : 0.003 0.029 2004 Dihedral : 7.882 78.440 1681 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.12 % Allowed : 15.97 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.37 (0.23), residues: 1410 helix: 1.82 (0.21), residues: 630 sheet: -1.32 (0.27), residues: 324 loop : -0.66 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.025 0.001 TYR B 219 PHE 0.011 0.001 PHE A 291 TRP 0.010 0.001 TRP C 214 HIS 0.002 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (12246) covalent geometry : angle 0.59714 / 0.28 (16701) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 0.88532 / 0.40 ( 12) hydrogen bonds : bond 0.04034 / 2.67 ( 594) hydrogen bonds : angle 4.07970 / 2.93 ( 1683) Misc. bond : bond 0.26392 / 13.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8214 (mm-30) REVERT: C 248 ARG cc_start: 0.8722 (mmm-85) cc_final: 0.8459 (mmm160) REVERT: C 274 TRP cc_start: 0.8018 (t-100) cc_final: 0.7347 (t-100) REVERT: C 279 ASP cc_start: 0.8865 (t0) cc_final: 0.8352 (t0) REVERT: C 292 MET cc_start: 0.8985 (mtm) cc_final: 0.8579 (mtt) REVERT: L 17 GLU cc_start: 0.8578 (tt0) cc_final: 0.8080 (tt0) REVERT: L 35 GLN cc_start: 0.8873 (mt0) cc_final: 0.8542 (mt0) REVERT: L 61 GLU cc_start: 0.8800 (tp30) cc_final: 0.8588 (tp30) REVERT: L 87 GLU cc_start: 0.8642 (pm20) cc_final: 0.8413 (pm20) REVERT: L 88 ASP cc_start: 0.8634 (m-30) cc_final: 0.8387 (m-30) REVERT: H 3 GLN cc_start: 0.8395 (tp40) cc_final: 0.7636 (tm-30) REVERT: H 5 GLN cc_start: 0.8863 (tt0) cc_final: 0.7810 (pp30) REVERT: H 13 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8338 (mmmt) REVERT: H 45 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8438 (tttp) REVERT: H 47 GLU cc_start: 0.9089 (tt0) cc_final: 0.8865 (tt0) REVERT: H 65 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8302 (ttpp) REVERT: H 73 ASP cc_start: 0.8222 (t0) cc_final: 0.8014 (t0) REVERT: H 82 GLN cc_start: 0.7891 (mp10) cc_final: 0.7530 (mp10) REVERT: H 89 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8937 (mp0) REVERT: H 100 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8147 (mtp85) REVERT: H 103 ASP cc_start: 0.8481 (t0) cc_final: 0.7760 (t70) REVERT: H 105 ASP cc_start: 0.8699 (m-30) cc_final: 0.8316 (m-30) REVERT: I 3 GLN cc_start: 0.8429 (tp40) cc_final: 0.7920 (tm-30) REVERT: I 5 GLN cc_start: 0.8820 (tt0) cc_final: 0.8229 (tm-30) REVERT: I 44 ASN cc_start: 0.8891 (m-40) cc_final: 0.8029 (p0) REVERT: I 45 LYS cc_start: 0.8651 (tttt) cc_final: 0.8368 (tttm) REVERT: I 73 ASP cc_start: 0.8138 (t0) cc_final: 0.7696 (t0) REVERT: I 100 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8243 (mmm-85) REVERT: I 103 ASP cc_start: 0.8427 (t0) cc_final: 0.7730 (t0) REVERT: I 105 ASP cc_start: 0.8759 (m-30) cc_final: 0.8404 (m-30) REVERT: J 3 GLN cc_start: 0.8348 (tp40) cc_final: 0.7910 (tp40) REVERT: J 5 GLN cc_start: 0.8694 (tt0) cc_final: 0.8052 (tm-30) REVERT: J 67 ARG cc_start: 0.8476 (ptt90) cc_final: 0.8026 (ptm-80) REVERT: J 73 ASP cc_start: 0.8218 (t0) cc_final: 0.7644 (t0) REVERT: J 89 GLU cc_start: 0.8453 (pm20) cc_final: 0.8210 (pp20) REVERT: J 90 ASP cc_start: 0.8159 (m-30) cc_final: 0.7446 (m-30) REVERT: J 100 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8434 (mmm-85) REVERT: J 103 ASP cc_start: 0.8477 (t0) cc_final: 0.7712 (t70) REVERT: J 105 ASP cc_start: 0.8677 (m-30) cc_final: 0.8284 (m-30) REVERT: M 17 GLU cc_start: 0.8673 (tt0) cc_final: 0.8430 (tt0) REVERT: M 85 LYS cc_start: 0.8531 (mttt) cc_final: 0.7994 (mtpm) REVERT: M 87 GLU cc_start: 0.8872 (pm20) cc_final: 0.8125 (pm20) REVERT: M 88 ASP cc_start: 0.8644 (m-30) cc_final: 0.8319 (m-30) REVERT: N 17 GLU cc_start: 0.8462 (tt0) cc_final: 0.7856 (tt0) REVERT: N 85 LYS cc_start: 0.8494 (mttt) cc_final: 0.8193 (mmmm) REVERT: N 87 GLU cc_start: 0.8946 (pm20) cc_final: 0.8595 (pm20) REVERT: A 104 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7283 (tp40) REVERT: A 274 TRP cc_start: 0.7851 (t-100) cc_final: 0.7247 (t-100) REVERT: A 279 ASP cc_start: 0.8936 (t0) cc_final: 0.8411 (t0) REVERT: B 93 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8252 (mm-30) REVERT: B 158 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8335 (tpp) REVERT: B 274 TRP cc_start: 0.8175 (t-100) cc_final: 0.7364 (t-100) REVERT: B 279 ASP cc_start: 0.9024 (t0) cc_final: 0.8492 (t0) REVERT: B 292 MET cc_start: 0.8799 (mtp) cc_final: 0.8434 (mtt) outliers start: 40 outliers final: 20 residues processed: 219 average time/residue: 0.6258 time to fit residues: 146.7846 Evaluate side-chains 208 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 97 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.055473 restraints weight = 25834.028| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.55 r_work: 0.2638 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.283 12255 Z= 0.144 Angle : 0.605 11.911 16713 Z= 0.283 Chirality : 0.041 0.168 1833 Planarity : 0.003 0.029 2004 Dihedral : 7.815 81.582 1680 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.88 % Allowed : 16.82 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.52 (0.23), residues: 1410 helix: 1.93 (0.21), residues: 630 sheet: -1.19 (0.28), residues: 324 loop : -0.61 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 248 TYR 0.026 0.001 TYR B 219 PHE 0.010 0.001 PHE A 291 TRP 0.009 0.001 TRP C 214 HIS 0.002 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 (12246) covalent geometry : angle 0.60418 / 0.28 (16701) SS BOND : bond 0.00246 / 0.12 ( 6) SS BOND : angle 0.96551 / 0.44 ( 12) hydrogen bonds : bond 0.04011 / 2.66 ( 594) hydrogen bonds : angle 4.02856 / 2.89 ( 1683) Misc. bond : bond 0.27207 / 13.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8246 (mm-30) REVERT: C 248 ARG cc_start: 0.8720 (mmm-85) cc_final: 0.8449 (mmm160) REVERT: C 274 TRP cc_start: 0.8087 (t-100) cc_final: 0.7371 (t-100) REVERT: C 279 ASP cc_start: 0.8877 (t0) cc_final: 0.8398 (t0) REVERT: C 292 MET cc_start: 0.8948 (mtm) cc_final: 0.8636 (mtt) REVERT: L 17 GLU cc_start: 0.8574 (tt0) cc_final: 0.8076 (tt0) REVERT: L 35 GLN cc_start: 0.8907 (mt0) cc_final: 0.8685 (mt0) REVERT: L 61 GLU cc_start: 0.8830 (tp30) cc_final: 0.8584 (tp30) REVERT: L 87 GLU cc_start: 0.8636 (pm20) cc_final: 0.8386 (pm20) REVERT: L 88 ASP cc_start: 0.8629 (m-30) cc_final: 0.8311 (m-30) REVERT: H 3 GLN cc_start: 0.8392 (tp40) cc_final: 0.7676 (tm-30) REVERT: H 5 GLN cc_start: 0.8770 (tt0) cc_final: 0.8069 (tm-30) REVERT: H 13 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8330 (mmmt) REVERT: H 45 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8432 (tttp) REVERT: H 47 GLU cc_start: 0.9080 (tt0) cc_final: 0.8822 (tt0) REVERT: H 65 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8293 (ttpp) REVERT: H 82 GLN cc_start: 0.7912 (mp10) cc_final: 0.7574 (mp10) REVERT: H 89 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8920 (mp0) REVERT: H 100 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8107 (mtp85) REVERT: H 103 ASP cc_start: 0.8484 (t0) cc_final: 0.7753 (t70) REVERT: H 105 ASP cc_start: 0.8719 (m-30) cc_final: 0.8325 (m-30) REVERT: I 3 GLN cc_start: 0.8418 (tp40) cc_final: 0.7833 (tm-30) REVERT: I 5 GLN cc_start: 0.8802 (tt0) cc_final: 0.8214 (tm-30) REVERT: I 44 ASN cc_start: 0.8884 (m-40) cc_final: 0.8032 (p0) REVERT: I 45 LYS cc_start: 0.8627 (tttt) cc_final: 0.8346 (tttm) REVERT: I 73 ASP cc_start: 0.8141 (t0) cc_final: 0.7687 (t0) REVERT: I 100 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8301 (mmm-85) REVERT: I 103 ASP cc_start: 0.8434 (t0) cc_final: 0.7726 (t0) REVERT: I 105 ASP cc_start: 0.8763 (m-30) cc_final: 0.8403 (m-30) REVERT: J 3 GLN cc_start: 0.8395 (tp40) cc_final: 0.7955 (tp40) REVERT: J 5 GLN cc_start: 0.8729 (tt0) cc_final: 0.8078 (tm-30) REVERT: J 67 ARG cc_start: 0.8588 (ptt90) cc_final: 0.8171 (ptm-80) REVERT: J 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7632 (t0) REVERT: J 90 ASP cc_start: 0.8183 (m-30) cc_final: 0.7975 (m-30) REVERT: J 100 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8405 (mmm-85) REVERT: J 103 ASP cc_start: 0.8489 (t0) cc_final: 0.7701 (t70) REVERT: J 105 ASP cc_start: 0.8658 (m-30) cc_final: 0.8265 (m-30) REVERT: M 17 GLU cc_start: 0.8668 (tt0) cc_final: 0.8407 (tt0) REVERT: M 61 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8355 (tp30) REVERT: M 85 LYS cc_start: 0.8502 (mttt) cc_final: 0.8001 (mtpm) REVERT: M 87 GLU cc_start: 0.8885 (pm20) cc_final: 0.8186 (pm20) REVERT: M 88 ASP cc_start: 0.8592 (m-30) cc_final: 0.8338 (m-30) REVERT: N 17 GLU cc_start: 0.8464 (tt0) cc_final: 0.7851 (tt0) REVERT: N 85 LYS cc_start: 0.8482 (mttt) cc_final: 0.8116 (mmmm) REVERT: N 87 GLU cc_start: 0.8933 (pm20) cc_final: 0.8588 (pm20) REVERT: A 93 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 104 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7296 (tp40) REVERT: A 274 TRP cc_start: 0.7783 (t-100) cc_final: 0.7249 (t-100) REVERT: A 279 ASP cc_start: 0.8927 (t0) cc_final: 0.8419 (t0) REVERT: B 93 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8235 (mm-30) REVERT: B 104 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: B 158 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8383 (tpp) REVERT: B 274 TRP cc_start: 0.8154 (t-100) cc_final: 0.7386 (t-100) REVERT: B 292 MET cc_start: 0.8755 (mtp) cc_final: 0.8376 (mtt) outliers start: 37 outliers final: 22 residues processed: 215 average time/residue: 0.6317 time to fit residues: 145.7803 Evaluate side-chains 212 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 53 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 16 GLN H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.055578 restraints weight = 25891.971| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.54 r_work: 0.2636 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.274 12255 Z= 0.144 Angle : 0.606 11.539 16713 Z= 0.283 Chirality : 0.041 0.170 1833 Planarity : 0.003 0.029 2004 Dihedral : 7.874 88.364 1680 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.57 % Allowed : 17.37 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.62 (0.23), residues: 1410 helix: 1.99 (0.21), residues: 630 sheet: -1.07 (0.28), residues: 324 loop : -0.58 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 248 TYR 0.025 0.001 TYR B 219 PHE 0.011 0.001 PHE A 291 TRP 0.011 0.001 TRP I 48 HIS 0.002 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (12246) covalent geometry : angle 0.60563 / 0.28 (16701) SS BOND : bond 0.00257 / 0.13 ( 6) SS BOND : angle 0.96362 / 0.44 ( 12) hydrogen bonds : bond 0.03951 / 2.62 ( 594) hydrogen bonds : angle 3.98174 / 2.85 ( 1683) Misc. bond : bond 0.26231 / 13.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8262 (mm-30) REVERT: C 248 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8433 (mmm160) REVERT: C 274 TRP cc_start: 0.8060 (t-100) cc_final: 0.7372 (t-100) REVERT: C 279 ASP cc_start: 0.8895 (t0) cc_final: 0.8394 (t0) REVERT: C 292 MET cc_start: 0.8951 (mtm) cc_final: 0.8480 (mtt) REVERT: L 17 GLU cc_start: 0.8572 (tt0) cc_final: 0.8064 (tt0) REVERT: L 35 GLN cc_start: 0.8894 (mt0) cc_final: 0.8654 (mt0) REVERT: L 61 GLU cc_start: 0.8818 (tp30) cc_final: 0.8569 (tp30) REVERT: L 87 GLU cc_start: 0.8653 (pm20) cc_final: 0.8404 (pm20) REVERT: L 88 ASP cc_start: 0.8653 (m-30) cc_final: 0.8353 (m-30) REVERT: H 3 GLN cc_start: 0.8393 (tp40) cc_final: 0.7667 (tm-30) REVERT: H 5 GLN cc_start: 0.8797 (tt0) cc_final: 0.7776 (pp30) REVERT: H 13 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8339 (mmmt) REVERT: H 36 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.9063 (m-40) REVERT: H 45 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8443 (tttp) REVERT: H 47 GLU cc_start: 0.9087 (tt0) cc_final: 0.8855 (tt0) REVERT: H 65 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8255 (ttpp) REVERT: H 82 GLN cc_start: 0.7886 (mp10) cc_final: 0.7300 (mp10) REVERT: H 89 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8925 (mp0) REVERT: H 100 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8225 (mmm-85) REVERT: H 103 ASP cc_start: 0.8468 (t0) cc_final: 0.7732 (t70) REVERT: H 105 ASP cc_start: 0.8705 (m-30) cc_final: 0.8309 (m-30) REVERT: I 3 GLN cc_start: 0.8403 (tp40) cc_final: 0.7811 (tm-30) REVERT: I 5 GLN cc_start: 0.8829 (tt0) cc_final: 0.8190 (tm-30) REVERT: I 44 ASN cc_start: 0.8920 (m-40) cc_final: 0.8104 (p0) REVERT: I 45 LYS cc_start: 0.8624 (tttt) cc_final: 0.8343 (tttm) REVERT: I 73 ASP cc_start: 0.8135 (t0) cc_final: 0.7673 (t0) REVERT: I 103 ASP cc_start: 0.8441 (t0) cc_final: 0.7718 (t0) REVERT: I 105 ASP cc_start: 0.8744 (m-30) cc_final: 0.8378 (m-30) REVERT: J 3 GLN cc_start: 0.8411 (tp40) cc_final: 0.7965 (tp40) REVERT: J 5 GLN cc_start: 0.8748 (tt0) cc_final: 0.8093 (tm-30) REVERT: J 67 ARG cc_start: 0.8523 (ptt90) cc_final: 0.8275 (ptt90) REVERT: J 73 ASP cc_start: 0.8192 (t0) cc_final: 0.7658 (t0) REVERT: J 100 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8405 (mmm-85) REVERT: J 103 ASP cc_start: 0.8499 (t0) cc_final: 0.7707 (t70) REVERT: J 105 ASP cc_start: 0.8688 (m-30) cc_final: 0.8284 (m-30) REVERT: M 17 GLU cc_start: 0.8668 (tt0) cc_final: 0.8405 (tt0) REVERT: M 85 LYS cc_start: 0.8502 (mttt) cc_final: 0.7980 (mtpm) REVERT: M 87 GLU cc_start: 0.8907 (pm20) cc_final: 0.8196 (pm20) REVERT: M 88 ASP cc_start: 0.8608 (m-30) cc_final: 0.8369 (m-30) REVERT: N 17 GLU cc_start: 0.8491 (tt0) cc_final: 0.7899 (tt0) REVERT: N 85 LYS cc_start: 0.8536 (mttt) cc_final: 0.8137 (mmmm) REVERT: N 87 GLU cc_start: 0.8955 (pm20) cc_final: 0.8614 (pm20) REVERT: A 93 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 120 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8603 (tpp) REVERT: A 274 TRP cc_start: 0.7898 (t-100) cc_final: 0.7372 (t-100) REVERT: A 279 ASP cc_start: 0.8935 (t0) cc_final: 0.8415 (t0) REVERT: B 93 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 104 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: B 158 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8323 (tpp) REVERT: B 274 TRP cc_start: 0.8156 (t-100) cc_final: 0.7391 (t-100) REVERT: B 292 MET cc_start: 0.8750 (mtp) cc_final: 0.8475 (mtt) outliers start: 33 outliers final: 18 residues processed: 206 average time/residue: 0.6521 time to fit residues: 143.9889 Evaluate side-chains 205 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.073197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.053971 restraints weight = 26061.843| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.57 r_work: 0.2598 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.339 12255 Z= 0.219 Angle : 0.660 13.821 16713 Z= 0.307 Chirality : 0.043 0.169 1833 Planarity : 0.004 0.030 2004 Dihedral : 8.015 87.204 1680 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.73 % Allowed : 17.21 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.57 (0.23), residues: 1410 helix: 1.90 (0.21), residues: 630 sheet: -1.05 (0.28), residues: 324 loop : -0.57 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 248 TYR 0.026 0.002 TYR B 219 PHE 0.009 0.001 PHE A 291 TRP 0.015 0.001 TRP H 35 HIS 0.004 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (12246) covalent geometry : angle 0.65912 / 0.31 (16701) SS BOND : bond 0.00318 / 0.16 ( 6) SS BOND : angle 1.35213 / 0.61 ( 12) hydrogen bonds : bond 0.04407 / 2.93 ( 594) hydrogen bonds : angle 4.09326 / 2.93 ( 1683) Misc. bond : bond 0.33194 / 16.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8279 (mm-30) REVERT: C 248 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8474 (mmm160) REVERT: C 274 TRP cc_start: 0.8082 (t-100) cc_final: 0.7384 (t-100) REVERT: C 279 ASP cc_start: 0.8907 (t0) cc_final: 0.8420 (t0) REVERT: C 292 MET cc_start: 0.8988 (mtm) cc_final: 0.8473 (mtt) REVERT: L 4 MET cc_start: 0.9140 (mmm) cc_final: 0.8634 (mmm) REVERT: L 17 GLU cc_start: 0.8577 (tt0) cc_final: 0.8053 (tt0) REVERT: L 35 GLN cc_start: 0.8951 (mt0) cc_final: 0.8700 (mt0) REVERT: L 61 GLU cc_start: 0.8828 (tp30) cc_final: 0.8574 (tp30) REVERT: L 87 GLU cc_start: 0.8643 (pm20) cc_final: 0.8387 (pm20) REVERT: L 88 ASP cc_start: 0.8668 (m-30) cc_final: 0.8367 (m-30) REVERT: H 3 GLN cc_start: 0.8415 (tp40) cc_final: 0.7699 (tm-30) REVERT: H 5 GLN cc_start: 0.8798 (tt0) cc_final: 0.7738 (pp30) REVERT: H 13 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8342 (mmmt) REVERT: H 36 ASN cc_start: 0.9516 (OUTLIER) cc_final: 0.9237 (m-40) REVERT: H 45 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8441 (tttp) REVERT: H 47 GLU cc_start: 0.9070 (tt0) cc_final: 0.8817 (tt0) REVERT: H 65 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8277 (ttpp) REVERT: H 82 GLN cc_start: 0.7834 (mp10) cc_final: 0.7445 (mp10) REVERT: H 89 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8939 (mp0) REVERT: H 100 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8144 (mtp85) REVERT: H 103 ASP cc_start: 0.8540 (t0) cc_final: 0.7812 (t70) REVERT: H 105 ASP cc_start: 0.8750 (m-30) cc_final: 0.8427 (m-30) REVERT: I 3 GLN cc_start: 0.8458 (tp40) cc_final: 0.7836 (tm-30) REVERT: I 5 GLN cc_start: 0.8817 (tt0) cc_final: 0.8219 (tm-30) REVERT: I 44 ASN cc_start: 0.8929 (m-40) cc_final: 0.8096 (p0) REVERT: I 45 LYS cc_start: 0.8646 (tttt) cc_final: 0.8363 (tttm) REVERT: I 73 ASP cc_start: 0.8160 (t0) cc_final: 0.7675 (t0) REVERT: I 103 ASP cc_start: 0.8478 (t0) cc_final: 0.7737 (t0) REVERT: I 105 ASP cc_start: 0.8777 (m-30) cc_final: 0.8401 (m-30) REVERT: J 3 GLN cc_start: 0.8424 (tp40) cc_final: 0.7957 (tp40) REVERT: J 5 GLN cc_start: 0.8781 (tt0) cc_final: 0.8124 (tm-30) REVERT: J 73 ASP cc_start: 0.8190 (t0) cc_final: 0.7605 (t0) REVERT: J 100 ARG cc_start: 0.8691 (mtp85) cc_final: 0.8451 (mmm-85) REVERT: J 103 ASP cc_start: 0.8569 (t0) cc_final: 0.7761 (t70) REVERT: J 105 ASP cc_start: 0.8642 (m-30) cc_final: 0.8238 (m-30) REVERT: M 17 GLU cc_start: 0.8626 (tt0) cc_final: 0.8341 (tt0) REVERT: M 85 LYS cc_start: 0.8466 (mttt) cc_final: 0.7878 (mtpm) REVERT: M 87 GLU cc_start: 0.8928 (pm20) cc_final: 0.8202 (pm20) REVERT: M 88 ASP cc_start: 0.8653 (m-30) cc_final: 0.8371 (m-30) REVERT: N 17 GLU cc_start: 0.8472 (tt0) cc_final: 0.7807 (tt0) REVERT: N 85 LYS cc_start: 0.8543 (mttt) cc_final: 0.8135 (mmmm) REVERT: N 87 GLU cc_start: 0.8981 (pm20) cc_final: 0.8640 (pm20) REVERT: A 93 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8159 (mm-30) REVERT: A 274 TRP cc_start: 0.8084 (t-100) cc_final: 0.7421 (t-100) REVERT: A 279 ASP cc_start: 0.8946 (t0) cc_final: 0.8432 (t0) REVERT: B 93 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8317 (mm-30) REVERT: B 104 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: B 158 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8408 (tpp) REVERT: B 274 TRP cc_start: 0.8159 (t-100) cc_final: 0.7404 (t-100) REVERT: B 279 ASP cc_start: 0.8939 (t0) cc_final: 0.8571 (t0) REVERT: B 292 MET cc_start: 0.8803 (mtp) cc_final: 0.8530 (mtt) outliers start: 35 outliers final: 20 residues processed: 207 average time/residue: 0.6862 time to fit residues: 152.0048 Evaluate side-chains 207 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 127 optimal weight: 0.0470 chunk 64 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.056365 restraints weight = 25857.858| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.56 r_work: 0.2647 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 12255 Z= 0.126 Angle : 0.606 10.571 16713 Z= 0.285 Chirality : 0.040 0.172 1833 Planarity : 0.004 0.031 2004 Dihedral : 7.797 89.476 1680 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.87 % Allowed : 17.91 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.72 (0.24), residues: 1410 helix: 2.06 (0.21), residues: 630 sheet: -0.98 (0.29), residues: 324 loop : -0.56 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 248 TYR 0.025 0.001 TYR B 219 PHE 0.010 0.001 PHE B 291 TRP 0.011 0.001 TRP A 277 HIS 0.002 0.000 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.12 (12246) covalent geometry : angle 0.60546 / 0.29 (16701) SS BOND : bond 0.00258 / 0.13 ( 6) SS BOND : angle 0.81811 / 0.38 ( 12) hydrogen bonds : bond 0.03818 / 2.53 ( 594) hydrogen bonds : angle 3.95522 / 2.82 ( 1683) Misc. bond : bond 0.23116 / 11.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8466 (mtp180) REVERT: C 93 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8181 (mm-30) REVERT: C 248 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8443 (mmm160) REVERT: C 274 TRP cc_start: 0.8074 (t-100) cc_final: 0.7403 (t-100) REVERT: C 279 ASP cc_start: 0.8908 (t0) cc_final: 0.8421 (t0) REVERT: C 292 MET cc_start: 0.8989 (mtm) cc_final: 0.8507 (mtt) REVERT: L 4 MET cc_start: 0.9087 (mmm) cc_final: 0.8756 (mmm) REVERT: L 17 GLU cc_start: 0.8576 (tt0) cc_final: 0.8056 (tt0) REVERT: L 35 GLN cc_start: 0.8871 (mt0) cc_final: 0.8618 (mt0) REVERT: L 61 GLU cc_start: 0.8782 (tp30) cc_final: 0.8549 (tp30) REVERT: L 87 GLU cc_start: 0.8672 (pm20) cc_final: 0.8403 (pm20) REVERT: L 88 ASP cc_start: 0.8656 (m-30) cc_final: 0.8372 (m-30) REVERT: H 3 GLN cc_start: 0.8369 (tp40) cc_final: 0.7677 (tm-30) REVERT: H 5 GLN cc_start: 0.8793 (tt0) cc_final: 0.7769 (pp30) REVERT: H 13 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8341 (mmmt) REVERT: H 27 TYR cc_start: 0.8295 (t80) cc_final: 0.8006 (t80) REVERT: H 32 ASP cc_start: 0.8440 (p0) cc_final: 0.8184 (p0) REVERT: H 45 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8420 (tttp) REVERT: H 47 GLU cc_start: 0.9098 (tt0) cc_final: 0.8843 (tt0) REVERT: H 65 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8256 (ttpp) REVERT: H 82 GLN cc_start: 0.7778 (mp10) cc_final: 0.7304 (mp10) REVERT: H 89 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8942 (mp0) REVERT: H 100 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8201 (mmm-85) REVERT: H 103 ASP cc_start: 0.8449 (t0) cc_final: 0.7731 (t70) REVERT: H 105 ASP cc_start: 0.8732 (m-30) cc_final: 0.8420 (m-30) REVERT: I 3 GLN cc_start: 0.8443 (tp40) cc_final: 0.7801 (tm-30) REVERT: I 5 GLN cc_start: 0.8808 (tt0) cc_final: 0.8175 (tm-30) REVERT: I 44 ASN cc_start: 0.8915 (m-40) cc_final: 0.8119 (p0) REVERT: I 45 LYS cc_start: 0.8615 (tttt) cc_final: 0.8335 (tttm) REVERT: I 73 ASP cc_start: 0.8151 (t0) cc_final: 0.7676 (t0) REVERT: I 103 ASP cc_start: 0.8413 (t0) cc_final: 0.7717 (t0) REVERT: I 105 ASP cc_start: 0.8753 (m-30) cc_final: 0.8384 (m-30) REVERT: J 3 GLN cc_start: 0.8397 (tp40) cc_final: 0.7974 (tp40) REVERT: J 5 GLN cc_start: 0.8766 (tt0) cc_final: 0.8107 (tm-30) REVERT: J 73 ASP cc_start: 0.8175 (t0) cc_final: 0.7599 (t0) REVERT: J 100 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8410 (mmm-85) REVERT: J 103 ASP cc_start: 0.8510 (t0) cc_final: 0.7730 (t70) REVERT: J 105 ASP cc_start: 0.8644 (m-30) cc_final: 0.8256 (m-30) REVERT: M 17 GLU cc_start: 0.8696 (tt0) cc_final: 0.8414 (tt0) REVERT: M 85 LYS cc_start: 0.8450 (mttt) cc_final: 0.7890 (mtpm) REVERT: M 87 GLU cc_start: 0.8931 (pm20) cc_final: 0.8242 (pm20) REVERT: M 88 ASP cc_start: 0.8631 (m-30) cc_final: 0.8388 (m-30) REVERT: N 17 GLU cc_start: 0.8494 (tt0) cc_final: 0.7870 (tt0) REVERT: N 85 LYS cc_start: 0.8565 (mttt) cc_final: 0.8274 (mmmm) REVERT: N 87 GLU cc_start: 0.8963 (pm20) cc_final: 0.8686 (pm20) REVERT: A 93 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 274 TRP cc_start: 0.7925 (t-100) cc_final: 0.7357 (t-100) REVERT: A 279 ASP cc_start: 0.8946 (t0) cc_final: 0.8425 (t0) REVERT: B 92 ARG cc_start: 0.8765 (mtp-110) cc_final: 0.8449 (mtp180) REVERT: B 93 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8213 (mm-30) REVERT: B 104 GLN cc_start: 0.7451 (mp10) cc_final: 0.7210 (mm-40) REVERT: B 158 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8350 (tpp) REVERT: B 274 TRP cc_start: 0.8129 (t-100) cc_final: 0.7384 (t-100) REVERT: B 279 ASP cc_start: 0.8953 (t0) cc_final: 0.8581 (t0) REVERT: B 292 MET cc_start: 0.8765 (mtp) cc_final: 0.8464 (mtt) outliers start: 24 outliers final: 19 residues processed: 216 average time/residue: 0.6448 time to fit residues: 149.2067 Evaluate side-chains 209 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 115 optimal weight: 0.0060 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 36 ASN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN J 44 ASN N 35 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.056904 restraints weight = 26082.248| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.59 r_work: 0.2665 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 12255 Z= 0.120 Angle : 0.601 11.856 16713 Z= 0.282 Chirality : 0.040 0.171 1833 Planarity : 0.004 0.033 2004 Dihedral : 7.463 81.442 1680 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.64 % Allowed : 18.22 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1410 helix: 2.12 (0.22), residues: 630 sheet: -0.95 (0.29), residues: 324 loop : -0.53 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 248 TYR 0.024 0.001 TYR B 219 PHE 0.011 0.001 PHE A 291 TRP 0.013 0.001 TRP A 214 HIS 0.002 0.000 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (12246) covalent geometry : angle 0.60025 / 0.28 (16701) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 0.90973 / 0.41 ( 12) hydrogen bonds : bond 0.03632 / 2.39 ( 594) hydrogen bonds : angle 3.90030 / 2.78 ( 1683) Misc. bond : bond 0.21590 / 10.84 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8121 (mm-30) REVERT: C 248 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8439 (mmm160) REVERT: C 274 TRP cc_start: 0.8066 (t-100) cc_final: 0.7406 (t-100) REVERT: C 279 ASP cc_start: 0.8915 (t0) cc_final: 0.8428 (t0) REVERT: C 292 MET cc_start: 0.8827 (mtm) cc_final: 0.8370 (mtt) REVERT: L 17 GLU cc_start: 0.8598 (tt0) cc_final: 0.8089 (tt0) REVERT: L 35 GLN cc_start: 0.8864 (mt0) cc_final: 0.8616 (mt0) REVERT: L 61 GLU cc_start: 0.8829 (tp30) cc_final: 0.8534 (tp30) REVERT: L 87 GLU cc_start: 0.8670 (pm20) cc_final: 0.8407 (pm20) REVERT: L 88 ASP cc_start: 0.8628 (m-30) cc_final: 0.8375 (m-30) REVERT: H 3 GLN cc_start: 0.8384 (tp40) cc_final: 0.7687 (tm-30) REVERT: H 5 GLN cc_start: 0.8780 (tt0) cc_final: 0.7951 (pp30) REVERT: H 13 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8356 (mmmt) REVERT: H 27 TYR cc_start: 0.8404 (t80) cc_final: 0.8165 (t80) REVERT: H 32 ASP cc_start: 0.8437 (p0) cc_final: 0.8188 (p0) REVERT: H 45 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8437 (tttp) REVERT: H 65 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8266 (ttpp) REVERT: H 82 GLN cc_start: 0.7826 (mp10) cc_final: 0.7386 (mp10) REVERT: H 89 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8931 (mp0) REVERT: H 100 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8184 (mmm-85) REVERT: H 103 ASP cc_start: 0.8422 (t0) cc_final: 0.7710 (t70) REVERT: H 105 ASP cc_start: 0.8720 (m-30) cc_final: 0.8331 (m-30) REVERT: I 3 GLN cc_start: 0.8443 (tp40) cc_final: 0.7795 (tm-30) REVERT: I 5 GLN cc_start: 0.8814 (tt0) cc_final: 0.8220 (tm-30) REVERT: I 44 ASN cc_start: 0.8902 (m-40) cc_final: 0.8076 (p0) REVERT: I 45 LYS cc_start: 0.8596 (tttt) cc_final: 0.8318 (tttm) REVERT: I 73 ASP cc_start: 0.8160 (t0) cc_final: 0.7709 (t0) REVERT: I 98 ARG cc_start: 0.8828 (ptt180) cc_final: 0.8446 (ptt90) REVERT: I 103 ASP cc_start: 0.8379 (t0) cc_final: 0.7686 (t0) REVERT: I 105 ASP cc_start: 0.8748 (m-30) cc_final: 0.8386 (m-30) REVERT: J 3 GLN cc_start: 0.8391 (tp40) cc_final: 0.7949 (tp40) REVERT: J 5 GLN cc_start: 0.8765 (tt0) cc_final: 0.8123 (tm-30) REVERT: J 73 ASP cc_start: 0.8219 (t0) cc_final: 0.7637 (t0) REVERT: J 103 ASP cc_start: 0.8482 (t0) cc_final: 0.7693 (t70) REVERT: J 105 ASP cc_start: 0.8639 (m-30) cc_final: 0.8235 (m-30) REVERT: M 17 GLU cc_start: 0.8711 (tt0) cc_final: 0.8445 (tt0) REVERT: M 85 LYS cc_start: 0.8412 (mttt) cc_final: 0.7837 (mtpm) REVERT: M 87 GLU cc_start: 0.8929 (pm20) cc_final: 0.8242 (pm20) REVERT: M 88 ASP cc_start: 0.8625 (m-30) cc_final: 0.8393 (m-30) REVERT: N 17 GLU cc_start: 0.8491 (tt0) cc_final: 0.7889 (tt0) REVERT: N 85 LYS cc_start: 0.8632 (mttt) cc_final: 0.8284 (mmmm) REVERT: N 87 GLU cc_start: 0.8940 (pm20) cc_final: 0.8675 (pm20) REVERT: A 93 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 212 ASP cc_start: 0.8643 (t70) cc_final: 0.8010 (t0) REVERT: A 274 TRP cc_start: 0.7962 (t-100) cc_final: 0.7439 (t-100) REVERT: A 279 ASP cc_start: 0.8958 (t0) cc_final: 0.8444 (t0) REVERT: B 92 ARG cc_start: 0.8763 (mtp-110) cc_final: 0.8495 (mtp180) REVERT: B 93 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8187 (mm-30) REVERT: B 104 GLN cc_start: 0.7429 (mp10) cc_final: 0.7186 (mm-40) REVERT: B 158 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8318 (tpp) REVERT: B 274 TRP cc_start: 0.8035 (t-100) cc_final: 0.7303 (t-100) REVERT: B 279 ASP cc_start: 0.8941 (t0) cc_final: 0.8572 (t0) REVERT: B 292 MET cc_start: 0.8752 (mtp) cc_final: 0.8450 (mtt) outliers start: 21 outliers final: 15 residues processed: 214 average time/residue: 0.6976 time to fit residues: 159.3958 Evaluate side-chains 209 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 ASN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.055131 restraints weight = 25858.829| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.56 r_work: 0.2634 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.295 12255 Z= 0.171 Angle : 0.650 12.648 16713 Z= 0.302 Chirality : 0.042 0.170 1833 Planarity : 0.004 0.032 2004 Dihedral : 7.573 78.459 1680 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.40 % Allowed : 19.00 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.75 (0.24), residues: 1410 helix: 2.05 (0.21), residues: 630 sheet: -0.91 (0.29), residues: 324 loop : -0.53 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 248 TYR 0.026 0.002 TYR B 219 PHE 0.008 0.001 PHE B 291 TRP 0.013 0.001 TRP A 214 HIS 0.003 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (12246) covalent geometry : angle 0.64986 / 0.30 (16701) SS BOND : bond 0.00343 / 0.17 ( 6) SS BOND : angle 1.16989 / 0.53 ( 12) hydrogen bonds : bond 0.04041 / 2.67 ( 594) hydrogen bonds : angle 3.96488 / 2.83 ( 1683) Misc. bond : bond 0.28958 / 14.50 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3777.98 seconds wall clock time: 65 minutes 18.90 seconds (3918.90 seconds total)