Starting phenix.real_space_refine on Sun Aug 24 05:22:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otq_17182/08_2025/8otq_17182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otq_17182/08_2025/8otq_17182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8otq_17182/08_2025/8otq_17182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otq_17182/08_2025/8otq_17182.map" model { file = "/net/cci-nas-00/data/ceres_data/8otq_17182/08_2025/8otq_17182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otq_17182/08_2025/8otq_17182.cif" } resolution = 3.22 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= 0.014 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 10942 2.51 5 N 2754 2.21 5 O 2932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16716 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 30, 'TRANS': 1020} Chain breaks: 3 Chain: "B" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 30, 'TRANS': 1020} Chain breaks: 3 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CPL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CPL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 3.60, per 1000 atoms: 0.22 Number of scatterers: 16716 At special positions: 0 Unit cell: (153.107, 105.074, 126.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 2 15.00 O 2932 8.00 N 2754 7.00 C 10942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 539.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3964 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 9 sheets defined 71.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.329A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.832A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 4.197A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.600A pdb=" N VAL A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.586A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.561A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.525A pdb=" N TRP A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 344 through 379 removed outlier: 3.783A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 406 removed outlier: 4.104A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.813A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 481 removed outlier: 3.826A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.723A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 575 through 601 Processing helix chain 'A' and resid 605 through 621 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 642 through 654 Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 677 through 703 removed outlier: 4.062A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 724 through 752 removed outlier: 3.590A pdb=" N ARG A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 741 " --> pdb=" O TYR A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.669A pdb=" N VAL A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 777 removed outlier: 3.713A pdb=" N ALA A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 813 through 858 Proline residue: A 819 - end of helix removed outlier: 3.810A pdb=" N ILE A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 823 " --> pdb=" O PRO A 819 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 889 removed outlier: 3.530A pdb=" N GLY A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.832A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.644A pdb=" N ALA A 927 " --> pdb=" O ASP A 923 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 960 removed outlier: 3.661A pdb=" N VAL A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 964 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.960A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix removed outlier: 4.231A pdb=" N MET A1104 " --> pdb=" O THR A1100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A1105 " --> pdb=" O PRO A1101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1124 removed outlier: 3.891A pdb=" N GLY A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.329A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.833A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 4.197A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.599A pdb=" N VAL B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.587A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.563A pdb=" N LEU B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 removed outlier: 3.526A pdb=" N TRP B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 317 Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 344 through 379 removed outlier: 3.782A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 406 removed outlier: 3.610A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.812A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 481 removed outlier: 3.826A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.714A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 575 through 601 Processing helix chain 'B' and resid 605 through 621 Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 642 through 654 Processing helix chain 'B' and resid 668 through 677 Processing helix chain 'B' and resid 677 through 703 removed outlier: 4.061A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 724 through 752 removed outlier: 3.590A pdb=" N ARG B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 741 " --> pdb=" O TYR B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.669A pdb=" N VAL B 760 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 removed outlier: 3.712A pdb=" N ALA B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 812 Processing helix chain 'B' and resid 813 through 858 Proline residue: B 819 - end of helix removed outlier: 3.810A pdb=" N ILE B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 823 " --> pdb=" O PRO B 819 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 889 removed outlier: 3.531A pdb=" N GLY B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.833A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.644A pdb=" N ALA B 927 " --> pdb=" O ASP B 923 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 960 removed outlier: 3.662A pdb=" N VAL B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 964 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.960A pdb=" N ILE B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix removed outlier: 4.231A pdb=" N MET B1104 " --> pdb=" O THR B1100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B1105 " --> pdb=" O PRO B1101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1124 removed outlier: 3.889A pdb=" N GLY B1124 " --> pdb=" O HIS B1120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.662A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.899A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.422A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A1149 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A1187 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A1147 " --> pdb=" O PHE A1187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1136 Processing sheet with id=AA5, first strand: chain 'A' and resid 1152 through 1153 Processing sheet with id=AA6, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.662A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.898A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.510A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B1149 " --> pdb=" O ARG B1185 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE B1187 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU B1147 " --> pdb=" O PHE B1187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1135 through 1137 removed outlier: 3.586A pdb=" N THR B1175 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B1153 " --> pdb=" O THR B1175 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2659 1.31 - 1.44: 4279 1.44 - 1.57: 9932 1.57 - 1.70: 6 1.70 - 1.82: 158 Bond restraints: 17034 Sorted by residual: bond pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 1.334 1.436 -0.102 1.27e-02 6.20e+03 6.45e+01 bond pdb=" C GLU B 847 " pdb=" N GLU B 848 " ideal model delta sigma weight residual 1.334 1.255 0.079 1.27e-02 6.20e+03 3.87e+01 bond pdb=" C GLU A 847 " pdb=" N GLU A 848 " ideal model delta sigma weight residual 1.334 1.256 0.078 1.27e-02 6.20e+03 3.78e+01 bond pdb=" C ARG A 499 " pdb=" N ARG A 500 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.27e-02 6.20e+03 2.61e+01 bond pdb=" C ARG B 499 " pdb=" N ARG B 500 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.27e-02 6.20e+03 2.61e+01 ... (remaining 17029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.10: 22962 5.10 - 10.21: 91 10.21 - 15.31: 13 15.31 - 20.41: 2 20.41 - 25.51: 2 Bond angle restraints: 23070 Sorted by residual: angle pdb=" C39 CPL A1401 " pdb=" C40 CPL A1401 " pdb=" C41 CPL A1401 " ideal model delta sigma weight residual 127.51 153.02 -25.51 3.00e+00 1.11e-01 7.23e+01 angle pdb=" C39 CPL B1401 " pdb=" C40 CPL B1401 " pdb=" C41 CPL B1401 " ideal model delta sigma weight residual 127.51 152.99 -25.48 3.00e+00 1.11e-01 7.21e+01 angle pdb=" O LEU B1086 " pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 122.12 128.95 -6.83 1.06e+00 8.90e-01 4.15e+01 angle pdb=" O GLU B1087 " pdb=" C GLU B1087 " pdb=" N TYR B1088 " ideal model delta sigma weight residual 122.07 128.45 -6.38 1.03e+00 9.43e-01 3.84e+01 angle pdb=" CA LEU B1086 " pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 117.30 110.42 6.88 1.16e+00 7.43e-01 3.52e+01 ... (remaining 23065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.72: 9521 30.72 - 61.45: 654 61.45 - 92.17: 37 92.17 - 122.89: 0 122.89 - 153.61: 6 Dihedral angle restraints: 10218 sinusoidal: 4100 harmonic: 6118 Sorted by residual: dihedral pdb=" C33 CPL B1401 " pdb=" C31 CPL B1401 " pdb=" C32 CPL B1401 " pdb=" O2 CPL B1401 " ideal model delta sinusoidal sigma weight residual 171.65 -34.74 -153.61 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C33 CPL A1401 " pdb=" C31 CPL A1401 " pdb=" C32 CPL A1401 " pdb=" O2 CPL A1401 " ideal model delta sinusoidal sigma weight residual 171.65 -34.74 -153.61 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C3 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C2 CPL B1401 " pdb=" O3P CPL B1401 " ideal model delta sinusoidal sigma weight residual 72.09 -73.31 145.40 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 10215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2053 0.048 - 0.096: 506 0.096 - 0.144: 148 0.144 - 0.192: 43 0.192 - 0.240: 12 Chirality restraints: 2762 Sorted by residual: chirality pdb=" C2 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C3 CPL B1401 " pdb=" O2 CPL B1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2 CPL A1401 " pdb=" C1 CPL A1401 " pdb=" C3 CPL A1401 " pdb=" O2 CPL A1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2759 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " -0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO B 642 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 642 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 732 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C LEU B 732 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 732 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 733 " -0.017 2.00e-02 2.50e+03 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 503 2.71 - 3.25: 17619 3.25 - 3.80: 26965 3.80 - 4.35: 30677 4.35 - 4.90: 52772 Nonbonded interactions: 128536 Sorted by model distance: nonbonded pdb=" N GLU A1071 " pdb=" OE1 GLU A1071 " model vdw 2.157 3.120 nonbonded pdb=" N GLU B1071 " pdb=" OE1 GLU B1071 " model vdw 2.158 3.120 nonbonded pdb=" N GLU A 346 " pdb=" OE1 GLU A 346 " model vdw 2.227 3.120 nonbonded pdb=" N GLU B 346 " pdb=" OE1 GLU B 346 " model vdw 2.227 3.120 nonbonded pdb=" N GLU A 531 " pdb=" OE1 GLU A 531 " model vdw 2.233 3.120 ... (remaining 128531 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 17034 Z= 0.349 Angle : 0.902 25.515 23070 Z= 0.507 Chirality : 0.050 0.240 2762 Planarity : 0.005 0.089 2828 Dihedral : 19.192 153.613 6254 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 2.99 % Allowed : 33.96 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.19), residues: 2086 helix: 1.84 (0.14), residues: 1354 sheet: 1.45 (0.64), residues: 54 loop : -1.87 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 585 TYR 0.029 0.001 TYR B 758 PHE 0.014 0.001 PHE A 598 TRP 0.019 0.001 TRP B 643 HIS 0.006 0.001 HIS B1172 Details of bonding type rmsd covalent geometry : bond 0.00557 (17034) covalent geometry : angle 0.90200 (23070) hydrogen bonds : bond 0.13286 ( 1106) hydrogen bonds : angle 5.15947 ( 3213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 PHE cc_start: 0.8556 (m-80) cc_final: 0.8332 (m-10) REVERT: A 678 MET cc_start: 0.7124 (pmm) cc_final: 0.6852 (pmm) REVERT: A 758 TYR cc_start: 0.8985 (t80) cc_final: 0.8773 (t80) REVERT: A 900 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: A 967 MET cc_start: 0.8986 (mmm) cc_final: 0.8483 (mpp) REVERT: A 986 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7546 (mt-10) REVERT: A 1109 PHE cc_start: 0.8651 (m-80) cc_final: 0.7919 (m-80) REVERT: A 1172 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5790 (m-70) REVERT: B 205 MET cc_start: 0.8712 (mtm) cc_final: 0.8504 (mtm) REVERT: B 477 LEU cc_start: 0.9464 (tp) cc_final: 0.9261 (tp) REVERT: B 967 MET cc_start: 0.8807 (mmm) cc_final: 0.8600 (mmm) REVERT: B 1109 PHE cc_start: 0.8616 (m-80) cc_final: 0.8118 (m-80) outliers start: 54 outliers final: 11 residues processed: 257 average time/residue: 0.1512 time to fit residues: 57.6638 Evaluate side-chains 189 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 677 HIS A 685 ASN A 691 ASN A 736 ASN A1120 HIS B 136 HIS B 677 HIS B 691 ASN B 736 ASN B 908 HIS B1120 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.110290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.075187 restraints weight = 44408.519| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.40 r_work: 0.3049 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17034 Z= 0.132 Angle : 0.587 8.521 23070 Z= 0.295 Chirality : 0.039 0.247 2762 Planarity : 0.005 0.085 2828 Dihedral : 11.152 144.128 2371 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.21 % Allowed : 32.08 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.19), residues: 2086 helix: 2.25 (0.14), residues: 1376 sheet: 1.27 (0.65), residues: 58 loop : -1.45 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 585 TYR 0.035 0.001 TYR B 758 PHE 0.014 0.001 PHE B1109 TRP 0.012 0.001 TRP B 635 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00295 (17034) covalent geometry : angle 0.58656 (23070) hydrogen bonds : bond 0.04698 ( 1106) hydrogen bonds : angle 3.85873 ( 3213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6343 (ptpp) REVERT: A 579 MET cc_start: 0.8023 (mmm) cc_final: 0.7754 (mmp) REVERT: A 662 MET cc_start: 0.7155 (mpp) cc_final: 0.6847 (tpt) REVERT: A 925 MET cc_start: 0.8460 (ppp) cc_final: 0.8061 (ppp) REVERT: A 967 MET cc_start: 0.9049 (mmm) cc_final: 0.8569 (mpp) REVERT: A 1172 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.6163 (m-70) REVERT: B 382 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6328 (ptpp) REVERT: B 662 MET cc_start: 0.6921 (mpp) cc_final: 0.6658 (tpt) REVERT: B 925 MET cc_start: 0.8395 (ppp) cc_final: 0.7976 (ppp) REVERT: B 967 MET cc_start: 0.9013 (mmm) cc_final: 0.8807 (mmm) outliers start: 58 outliers final: 23 residues processed: 220 average time/residue: 0.1157 time to fit residues: 41.1101 Evaluate side-chains 189 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN A 764 ASN B 685 ASN B 702 GLN B 908 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.072859 restraints weight = 45089.446| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.53 r_work: 0.3000 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17034 Z= 0.142 Angle : 0.551 6.779 23070 Z= 0.281 Chirality : 0.038 0.183 2762 Planarity : 0.004 0.084 2828 Dihedral : 10.377 143.463 2347 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.15 % Allowed : 30.86 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.19), residues: 2086 helix: 2.48 (0.14), residues: 1368 sheet: 1.25 (0.65), residues: 58 loop : -1.40 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 585 TYR 0.016 0.001 TYR A 758 PHE 0.019 0.001 PHE A 769 TRP 0.017 0.001 TRP B 635 HIS 0.004 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00322 (17034) covalent geometry : angle 0.55140 (23070) hydrogen bonds : bond 0.04839 ( 1106) hydrogen bonds : angle 3.70461 ( 3213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8200 (mpp) cc_final: 0.7950 (mpp) REVERT: A 581 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8457 (pp20) REVERT: A 662 MET cc_start: 0.7227 (mpp) cc_final: 0.6928 (tpt) REVERT: A 857 MET cc_start: 0.8524 (tmm) cc_final: 0.7896 (tmm) REVERT: A 967 MET cc_start: 0.9011 (mmm) cc_final: 0.8555 (mpp) REVERT: B 511 MET cc_start: 0.9438 (tmm) cc_final: 0.9184 (tmm) REVERT: B 662 MET cc_start: 0.7104 (mpp) cc_final: 0.6833 (tpt) REVERT: B 1107 MET cc_start: 0.6675 (tmm) cc_final: 0.6392 (tmm) REVERT: B 1169 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.6140 (ttt-90) outliers start: 57 outliers final: 27 residues processed: 220 average time/residue: 0.1046 time to fit residues: 37.1433 Evaluate side-chains 186 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 ASN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.109137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073945 restraints weight = 44761.877| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.52 r_work: 0.3019 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17034 Z= 0.113 Angle : 0.529 7.477 23070 Z= 0.266 Chirality : 0.037 0.135 2762 Planarity : 0.004 0.083 2828 Dihedral : 10.096 142.777 2345 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.71 % Allowed : 31.42 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.19), residues: 2086 helix: 2.58 (0.14), residues: 1366 sheet: 1.47 (0.64), residues: 58 loop : -1.30 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 585 TYR 0.011 0.001 TYR A 758 PHE 0.016 0.001 PHE A1109 TRP 0.018 0.001 TRP B 635 HIS 0.007 0.001 HIS A1172 Details of bonding type rmsd covalent geometry : bond 0.00242 (17034) covalent geometry : angle 0.52914 (23070) hydrogen bonds : bond 0.04395 ( 1106) hydrogen bonds : angle 3.57257 ( 3213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.8157 (mpp) cc_final: 0.7723 (mpp) REVERT: A 662 MET cc_start: 0.7218 (mpp) cc_final: 0.6970 (tpt) REVERT: A 737 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.7025 (m-10) REVERT: A 967 MET cc_start: 0.8982 (mmm) cc_final: 0.8539 (mpp) REVERT: B 578 MET cc_start: 0.8160 (mpp) cc_final: 0.7811 (mpp) REVERT: B 662 MET cc_start: 0.7029 (mpp) cc_final: 0.6739 (tpt) REVERT: B 685 ASN cc_start: 0.8037 (m110) cc_final: 0.7602 (p0) REVERT: B 1107 MET cc_start: 0.6689 (tmm) cc_final: 0.6462 (tmm) REVERT: B 1109 PHE cc_start: 0.8764 (m-80) cc_final: 0.8527 (m-80) outliers start: 49 outliers final: 30 residues processed: 203 average time/residue: 0.0987 time to fit residues: 32.8584 Evaluate side-chains 190 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 139 optimal weight: 0.3980 chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.109416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074475 restraints weight = 44586.522| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.52 r_work: 0.3037 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17034 Z= 0.107 Angle : 0.515 10.646 23070 Z= 0.258 Chirality : 0.037 0.136 2762 Planarity : 0.004 0.082 2828 Dihedral : 9.849 141.708 2345 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.10 % Allowed : 30.48 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.19), residues: 2086 helix: 2.69 (0.14), residues: 1366 sheet: 1.59 (0.64), residues: 58 loop : -1.23 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 585 TYR 0.010 0.001 TYR B 312 PHE 0.018 0.001 PHE A 769 TRP 0.014 0.001 TRP B 635 HIS 0.004 0.000 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00230 (17034) covalent geometry : angle 0.51535 (23070) hydrogen bonds : bond 0.04118 ( 1106) hydrogen bonds : angle 3.50692 ( 3213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.548 Fit side-chains REVERT: A 578 MET cc_start: 0.8044 (mpp) cc_final: 0.7805 (mpp) REVERT: A 737 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.7114 (m-10) REVERT: A 967 MET cc_start: 0.8967 (mmm) cc_final: 0.8727 (mmm) REVERT: A 1107 MET cc_start: 0.6791 (tmm) cc_final: 0.6426 (ppp) REVERT: A 1109 PHE cc_start: 0.8696 (m-80) cc_final: 0.8478 (m-80) REVERT: B 579 MET cc_start: 0.8213 (mmm) cc_final: 0.7946 (mmp) REVERT: B 670 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6526 (mp) REVERT: B 685 ASN cc_start: 0.8042 (m110) cc_final: 0.7632 (p0) REVERT: B 737 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: B 1107 MET cc_start: 0.6700 (tmm) cc_final: 0.6406 (tmm) REVERT: B 1109 PHE cc_start: 0.8735 (m-80) cc_final: 0.8485 (m-80) outliers start: 56 outliers final: 30 residues processed: 215 average time/residue: 0.0991 time to fit residues: 35.1621 Evaluate side-chains 194 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 737 TYR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 136 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 172 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS B 736 ASN ** B1172 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.109337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074452 restraints weight = 44743.172| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.50 r_work: 0.3028 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17034 Z= 0.110 Angle : 0.526 8.191 23070 Z= 0.263 Chirality : 0.037 0.150 2762 Planarity : 0.004 0.092 2828 Dihedral : 9.719 140.810 2345 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.21 % Allowed : 30.31 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.19), residues: 2086 helix: 2.73 (0.14), residues: 1364 sheet: 1.30 (0.63), residues: 62 loop : -1.18 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 585 TYR 0.010 0.001 TYR B 312 PHE 0.015 0.001 PHE A 769 TRP 0.019 0.001 TRP B 635 HIS 0.003 0.000 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00240 (17034) covalent geometry : angle 0.52608 (23070) hydrogen bonds : bond 0.04114 ( 1106) hydrogen bonds : angle 3.49286 ( 3213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 578 MET cc_start: 0.7992 (mpp) cc_final: 0.7638 (mpp) REVERT: A 670 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6239 (mp) REVERT: A 737 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: A 857 MET cc_start: 0.8379 (tmm) cc_final: 0.8045 (tmm) REVERT: A 967 MET cc_start: 0.8985 (mmm) cc_final: 0.8747 (mmm) REVERT: A 1107 MET cc_start: 0.6983 (tmm) cc_final: 0.6641 (ppp) REVERT: A 1109 PHE cc_start: 0.8733 (m-80) cc_final: 0.8517 (m-80) REVERT: A 1172 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6413 (m-70) REVERT: B 579 MET cc_start: 0.8328 (mmm) cc_final: 0.8098 (mmp) REVERT: B 685 ASN cc_start: 0.8129 (m110) cc_final: 0.7727 (p0) REVERT: B 737 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.7040 (m-10) outliers start: 58 outliers final: 34 residues processed: 214 average time/residue: 0.1053 time to fit residues: 36.6558 Evaluate side-chains 195 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 737 TYR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1148 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 45 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 736 ASN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074045 restraints weight = 44650.020| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.51 r_work: 0.3014 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17034 Z= 0.121 Angle : 0.543 15.983 23070 Z= 0.269 Chirality : 0.037 0.157 2762 Planarity : 0.004 0.094 2828 Dihedral : 9.620 140.351 2344 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.71 % Allowed : 30.53 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.19), residues: 2086 helix: 2.74 (0.14), residues: 1364 sheet: 1.39 (0.63), residues: 62 loop : -1.24 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 585 TYR 0.013 0.001 TYR B 641 PHE 0.018 0.001 PHE B 769 TRP 0.018 0.001 TRP B 635 HIS 0.003 0.000 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00270 (17034) covalent geometry : angle 0.54250 (23070) hydrogen bonds : bond 0.04262 ( 1106) hydrogen bonds : angle 3.50718 ( 3213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.459 Fit side-chains REVERT: A 578 MET cc_start: 0.8039 (mpp) cc_final: 0.7686 (mpp) REVERT: A 737 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: A 857 MET cc_start: 0.8416 (tmm) cc_final: 0.8069 (tmm) REVERT: A 967 MET cc_start: 0.8993 (mmm) cc_final: 0.8764 (mmm) REVERT: A 1107 MET cc_start: 0.6928 (tmm) cc_final: 0.6597 (ppp) REVERT: A 1172 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.6408 (m-70) REVERT: B 579 MET cc_start: 0.8346 (mmm) cc_final: 0.8136 (mmp) REVERT: B 1169 ARG cc_start: 0.6871 (ttt180) cc_final: 0.6634 (ttt180) outliers start: 49 outliers final: 34 residues processed: 201 average time/residue: 0.0959 time to fit residues: 31.8936 Evaluate side-chains 189 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1148 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 174 optimal weight: 0.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 ASN B 736 ASN ** B1172 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.108806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074464 restraints weight = 44074.436| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.40 r_work: 0.3026 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17034 Z= 0.117 Angle : 0.551 13.990 23070 Z= 0.272 Chirality : 0.038 0.191 2762 Planarity : 0.004 0.093 2828 Dihedral : 9.534 139.885 2344 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.32 % Allowed : 30.70 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.19), residues: 2086 helix: 2.72 (0.14), residues: 1378 sheet: 1.41 (0.63), residues: 62 loop : -1.25 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.010 0.001 TYR B 312 PHE 0.018 0.001 PHE B 699 TRP 0.019 0.001 TRP A 635 HIS 0.003 0.000 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00260 (17034) covalent geometry : angle 0.55117 (23070) hydrogen bonds : bond 0.04224 ( 1106) hydrogen bonds : angle 3.50515 ( 3213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.547 Fit side-chains REVERT: A 578 MET cc_start: 0.8042 (mpp) cc_final: 0.7668 (mpp) REVERT: A 737 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: A 857 MET cc_start: 0.8419 (tmm) cc_final: 0.8071 (tmm) REVERT: A 967 MET cc_start: 0.8955 (mmm) cc_final: 0.8726 (mmm) REVERT: A 1107 MET cc_start: 0.6925 (tmm) cc_final: 0.6589 (ppp) REVERT: A 1172 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6453 (m-70) REVERT: B 579 MET cc_start: 0.8356 (mmm) cc_final: 0.8148 (mmp) REVERT: B 670 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6433 (mp) REVERT: B 1107 MET cc_start: 0.6816 (tmm) cc_final: 0.6533 (tmm) REVERT: B 1169 ARG cc_start: 0.6839 (ttt180) cc_final: 0.6473 (ttt180) outliers start: 42 outliers final: 32 residues processed: 192 average time/residue: 0.0991 time to fit residues: 31.1601 Evaluate side-chains 186 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1148 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 190 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.108337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073497 restraints weight = 44427.964| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.43 r_work: 0.3012 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17034 Z= 0.125 Angle : 0.558 12.432 23070 Z= 0.278 Chirality : 0.038 0.152 2762 Planarity : 0.004 0.092 2828 Dihedral : 9.454 139.506 2344 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.21 % Allowed : 30.92 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.19), residues: 2086 helix: 2.73 (0.14), residues: 1376 sheet: 1.41 (0.63), residues: 62 loop : -1.26 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 585 TYR 0.011 0.001 TYR B 312 PHE 0.020 0.001 PHE B 769 TRP 0.020 0.001 TRP B 635 HIS 0.003 0.000 HIS B 600 Details of bonding type rmsd covalent geometry : bond 0.00284 (17034) covalent geometry : angle 0.55802 (23070) hydrogen bonds : bond 0.04360 ( 1106) hydrogen bonds : angle 3.53582 ( 3213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.425 Fit side-chains REVERT: A 578 MET cc_start: 0.8024 (mpp) cc_final: 0.7634 (mpp) REVERT: A 737 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: A 857 MET cc_start: 0.8404 (tmm) cc_final: 0.8033 (tmm) REVERT: A 967 MET cc_start: 0.8961 (mmm) cc_final: 0.8569 (mmm) REVERT: A 1107 MET cc_start: 0.6956 (tmm) cc_final: 0.6611 (ppp) REVERT: B 670 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6454 (mp) REVERT: B 1107 MET cc_start: 0.6840 (tmm) cc_final: 0.6559 (tmm) outliers start: 40 outliers final: 33 residues processed: 191 average time/residue: 0.0946 time to fit residues: 29.1710 Evaluate side-chains 186 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1148 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 19 optimal weight: 2.9990 chunk 169 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.110240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.075629 restraints weight = 44597.603| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.44 r_work: 0.3055 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17034 Z= 0.108 Angle : 0.558 11.442 23070 Z= 0.275 Chirality : 0.037 0.203 2762 Planarity : 0.004 0.092 2828 Dihedral : 9.287 138.977 2344 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.88 % Allowed : 31.25 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.19), residues: 2086 helix: 2.77 (0.14), residues: 1376 sheet: 1.55 (0.64), residues: 62 loop : -1.30 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.008 0.001 TYR B 312 PHE 0.022 0.001 PHE B 699 TRP 0.018 0.001 TRP A 635 HIS 0.004 0.000 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00229 (17034) covalent geometry : angle 0.55787 (23070) hydrogen bonds : bond 0.03822 ( 1106) hydrogen bonds : angle 3.46679 ( 3213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.418 Fit side-chains REVERT: A 578 MET cc_start: 0.8009 (mpp) cc_final: 0.7618 (mpp) REVERT: A 737 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: A 967 MET cc_start: 0.8968 (mmm) cc_final: 0.8585 (mmm) REVERT: A 1107 MET cc_start: 0.6910 (tmm) cc_final: 0.6554 (ppp) REVERT: A 1172 HIS cc_start: 0.6817 (OUTLIER) cc_final: 0.6480 (m-70) REVERT: B 670 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6435 (mp) REVERT: B 1107 MET cc_start: 0.6813 (tmm) cc_final: 0.6525 (tmm) outliers start: 34 outliers final: 28 residues processed: 190 average time/residue: 0.0983 time to fit residues: 30.6198 Evaluate side-chains 183 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074393 restraints weight = 44192.256| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.48 r_work: 0.3031 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17034 Z= 0.117 Angle : 0.560 11.137 23070 Z= 0.277 Chirality : 0.038 0.177 2762 Planarity : 0.004 0.091 2828 Dihedral : 9.173 138.396 2344 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.77 % Allowed : 31.53 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.19), residues: 2086 helix: 2.80 (0.14), residues: 1372 sheet: 1.59 (0.64), residues: 62 loop : -1.27 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.011 0.001 TYR B 312 PHE 0.020 0.001 PHE B 769 TRP 0.017 0.001 TRP B 635 HIS 0.003 0.000 HIS B1172 Details of bonding type rmsd covalent geometry : bond 0.00259 (17034) covalent geometry : angle 0.56036 (23070) hydrogen bonds : bond 0.04089 ( 1106) hydrogen bonds : angle 3.49034 ( 3213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.52 seconds wall clock time: 73 minutes 34.62 seconds (4414.62 seconds total)