Starting phenix.real_space_refine on Sun Jun 15 11:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otq_17182/06_2025/8otq_17182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otq_17182/06_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_17182/06_2025/8otq_17182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otq_17182/06_2025/8otq_17182.map" model { file = "/net/cci-nas-00/data/ceres_data/8otq_17182/06_2025/8otq_17182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otq_17182/06_2025/8otq_17182.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.42, per 1000 atoms: 0.62 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: 4.21 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.79 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: 5.40 Time building geometry restraints manager: 4.97 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: 0.08 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.470 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP B 643 HIS 0.006 0.001 HIS B1172 PHE 0.014 0.001 PHE A 598 TYR 0.029 0.001 TYR B 758 ARG 0.004 0.000 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.13286 ( 1106) hydrogen bonds : angle 5.15947 ( 3213) covalent geometry : bond 0.00557 (17034) covalent geometry : angle 0.90200 (23070) *********************** 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 : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.7124 (pmm) cc_final: 0.6851 (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: 0.8191 (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: 0.5791 (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: 0.8117 (m-80) outliers start: 54 outliers final: 11 residues processed: 257 average time/residue: 0.3081 time to fit residues: 117.9661 Evaluate side-chains 188 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 177 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 764 ASN 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 = 0.3788 r_free = 0.3788 target = 0.108088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072599 restraints weight = 44807.995| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.44 r_work: 0.2993 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17034 Z= 0.166 Angle : 0.606 8.084 23070 Z= 0.306 Chirality : 0.039 0.189 2762 Planarity : 0.005 0.085 2828 Dihedral : 11.168 144.205 2371 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.76 % Allowed : 31.64 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2086 helix: 2.18 (0.14), residues: 1376 sheet: 1.16 (0.64), residues: 58 loop : -1.45 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 643 HIS 0.003 0.001 HIS B1172 PHE 0.013 0.001 PHE B 625 TYR 0.034 0.001 TYR B 758 ARG 0.008 0.001 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 1106) hydrogen bonds : angle 3.95047 ( 3213) covalent geometry : bond 0.00385 (17034) covalent geometry : angle 0.60584 (23070) *********************** 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 242 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: A 382 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6360 (ptpp) REVERT: A 579 MET cc_start: 0.8049 (mmm) cc_final: 0.7776 (mmp) REVERT: A 662 MET cc_start: 0.7276 (mpp) cc_final: 0.7003 (tpt) REVERT: A 925 MET cc_start: 0.8485 (ppp) cc_final: 0.7911 (ppp) REVERT: A 967 MET cc_start: 0.9062 (mmm) cc_final: 0.8592 (mpp) REVERT: B 382 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6371 (ptpp) REVERT: B 925 MET cc_start: 0.8424 (ppp) cc_final: 0.8011 (ppp) REVERT: B 967 MET cc_start: 0.9015 (mmm) cc_final: 0.8806 (mmm) outliers start: 68 outliers final: 32 residues processed: 223 average time/residue: 0.2408 time to fit residues: 86.2359 Evaluate side-chains 190 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 298 LEU 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 425 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE 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 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 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 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL 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 39 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN B 702 GLN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.072929 restraints weight = 44285.922| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.50 r_work: 0.2995 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17034 Z= 0.133 Angle : 0.548 6.707 23070 Z= 0.280 Chirality : 0.038 0.175 2762 Planarity : 0.004 0.084 2828 Dihedral : 10.308 143.882 2345 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.10 % Allowed : 31.36 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2086 helix: 2.44 (0.14), residues: 1370 sheet: 1.25 (0.65), residues: 58 loop : -1.43 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 635 HIS 0.004 0.001 HIS B 677 PHE 0.014 0.001 PHE A 769 TYR 0.016 0.001 TYR A 758 ARG 0.004 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 1106) hydrogen bonds : angle 3.70488 ( 3213) covalent geometry : bond 0.00291 (17034) covalent geometry : angle 0.54768 (23070) *********************** 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 225 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6245 (ptpp) REVERT: A 578 MET cc_start: 0.8202 (mpp) cc_final: 0.7957 (mpp) REVERT: A 662 MET cc_start: 0.7290 (mpp) cc_final: 0.7008 (tpt) REVERT: A 857 MET cc_start: 0.8536 (tmm) cc_final: 0.8170 (tmm) REVERT: A 967 MET cc_start: 0.9012 (mmm) cc_final: 0.8562 (mpp) REVERT: A 1109 PHE cc_start: 0.8693 (m-80) cc_final: 0.8483 (m-80) REVERT: B 578 MET cc_start: 0.8101 (mpp) cc_final: 0.7800 (mpp) REVERT: B 579 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7722 (mmp) REVERT: B 967 MET cc_start: 0.8995 (mmm) cc_final: 0.8636 (mmm) REVERT: B 1107 MET cc_start: 0.6718 (tmm) cc_final: 0.6461 (tmm) outliers start: 56 outliers final: 21 residues processed: 215 average time/residue: 0.2340 time to fit residues: 82.3406 Evaluate side-chains 182 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 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 1057 VAL 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 579 MET 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 1057 VAL 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 43 optimal weight: 3.9990 chunk 157 optimal weight: 0.0470 chunk 159 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 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 = 0.3793 r_free = 0.3793 target = 0.108130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072855 restraints weight = 44709.472| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.45 r_work: 0.2956 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2079 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= 0.123 Angle : 0.526 7.669 23070 Z= 0.267 Chirality : 0.037 0.134 2762 Planarity : 0.004 0.083 2828 Dihedral : 10.060 142.906 2345 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.26 % Allowed : 30.92 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.19), residues: 2086 helix: 2.55 (0.14), residues: 1368 sheet: 1.39 (0.63), residues: 58 loop : -1.33 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 635 HIS 0.004 0.001 HIS A 600 PHE 0.017 0.001 PHE A 769 TYR 0.011 0.001 TYR B 312 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1106) hydrogen bonds : angle 3.61451 ( 3213) covalent geometry : bond 0.00271 (17034) covalent geometry : angle 0.52555 (23070) *********************** 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 223 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 2.027 Fit side-chains revert: symmetry clash REVERT: A 578 MET cc_start: 0.8012 (mpp) cc_final: 0.7772 (mpp) REVERT: A 662 MET cc_start: 0.7300 (mpp) cc_final: 0.7057 (tpt) REVERT: A 737 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: A 857 MET cc_start: 0.8574 (tmm) cc_final: 0.7862 (tmm) REVERT: A 967 MET cc_start: 0.9004 (mmm) cc_final: 0.8764 (mmm) REVERT: B 578 MET cc_start: 0.7972 (mpp) cc_final: 0.7722 (mpp) REVERT: B 685 ASN cc_start: 0.7998 (m110) cc_final: 0.7608 (p0) REVERT: B 967 MET cc_start: 0.8994 (mmm) cc_final: 0.8640 (mmm) REVERT: B 1107 MET cc_start: 0.6877 (tmm) cc_final: 0.6609 (tmm) outliers start: 59 outliers final: 32 residues processed: 212 average time/residue: 0.2622 time to fit residues: 88.9394 Evaluate side-chains 189 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 373 THR 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 833 LEU Chi-restraints excluded: chain A residue 850 VAL 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 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 627 LEU 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 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 148 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.108637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073574 restraints weight = 44948.197| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.52 r_work: 0.3010 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17034 Z= 0.113 Angle : 0.521 7.867 23070 Z= 0.263 Chirality : 0.037 0.135 2762 Planarity : 0.004 0.091 2828 Dihedral : 9.864 142.268 2345 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.54 % Allowed : 30.20 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.19), residues: 2086 helix: 2.64 (0.14), residues: 1366 sheet: 1.49 (0.63), residues: 58 loop : -1.27 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 635 HIS 0.003 0.000 HIS A 600 PHE 0.018 0.001 PHE A 769 TYR 0.027 0.001 TYR B 641 ARG 0.004 0.000 ARG B1158 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 1106) hydrogen bonds : angle 3.54031 ( 3213) covalent geometry : bond 0.00243 (17034) covalent geometry : angle 0.52131 (23070) *********************** 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 220 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 1.900 Fit side-chains REVERT: A 578 MET cc_start: 0.8009 (mpp) cc_final: 0.7787 (mpp) REVERT: A 737 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.7115 (m-10) REVERT: A 857 MET cc_start: 0.8453 (tmm) cc_final: 0.8055 (tmm) REVERT: A 967 MET cc_start: 0.8944 (mmm) cc_final: 0.8705 (mmm) REVERT: A 1172 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6425 (m-70) REVERT: B 578 MET cc_start: 0.8003 (mpp) cc_final: 0.7694 (mpp) REVERT: B 670 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6592 (mp) REVERT: B 685 ASN cc_start: 0.8027 (m110) cc_final: 0.7625 (p0) REVERT: B 737 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6898 (m-10) REVERT: B 967 MET cc_start: 0.8959 (mmm) cc_final: 0.8610 (mmm) REVERT: B 1107 MET cc_start: 0.6774 (tmm) cc_final: 0.6491 (tmm) REVERT: B 1169 ARG cc_start: 0.6852 (ttt180) cc_final: 0.6591 (ttt180) outliers start: 64 outliers final: 36 residues processed: 210 average time/residue: 0.2431 time to fit residues: 83.1637 Evaluate side-chains 193 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 373 THR 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 850 VAL 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 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 373 THR Chi-restraints excluded: chain B residue 468 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 181 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3770 r_free = 0.3770 target = 0.107026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071856 restraints weight = 44926.282| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.52 r_work: 0.2972 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.143 Angle : 0.547 14.616 23070 Z= 0.274 Chirality : 0.038 0.134 2762 Planarity : 0.004 0.093 2828 Dihedral : 9.771 142.077 2345 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.48 % Allowed : 30.20 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 2086 helix: 2.66 (0.14), residues: 1364 sheet: 1.55 (0.64), residues: 58 loop : -1.26 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 635 HIS 0.004 0.000 HIS A 600 PHE 0.015 0.001 PHE A 769 TYR 0.014 0.001 TYR B 641 ARG 0.003 0.000 ARG B1158 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 1106) hydrogen bonds : angle 3.60625 ( 3213) covalent geometry : bond 0.00328 (17034) covalent geometry : angle 0.54737 (23070) *********************** 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 223 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 578 MET cc_start: 0.7996 (mpp) cc_final: 0.7633 (mpp) REVERT: A 670 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6245 (mp) REVERT: A 737 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: A 857 MET cc_start: 0.8505 (tmm) cc_final: 0.8075 (tmm) REVERT: A 967 MET cc_start: 0.8968 (mmm) cc_final: 0.8742 (mmm) REVERT: A 1107 MET cc_start: 0.6979 (tmm) cc_final: 0.6682 (ppp) REVERT: A 1172 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.6564 (m-70) REVERT: B 578 MET cc_start: 0.8004 (mpp) cc_final: 0.7696 (mpp) REVERT: B 967 MET cc_start: 0.8961 (mmm) cc_final: 0.8607 (mmm) REVERT: B 1107 MET cc_start: 0.6769 (tmm) cc_final: 0.6479 (tmm) outliers start: 63 outliers final: 36 residues processed: 214 average time/residue: 0.2463 time to fit residues: 85.4899 Evaluate side-chains 194 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 322 SER Chi-restraints excluded: chain A residue 373 THR 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 850 VAL 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 1148 ILE 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 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 644 LEU 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 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 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 101 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS A 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 = 0.3769 r_free = 0.3769 target = 0.107001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071900 restraints weight = 44697.927| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.50 r_work: 0.2976 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17034 Z= 0.139 Angle : 0.555 11.936 23070 Z= 0.277 Chirality : 0.038 0.176 2762 Planarity : 0.004 0.092 2828 Dihedral : 9.697 142.352 2345 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.15 % Allowed : 30.64 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 2086 helix: 2.65 (0.14), residues: 1374 sheet: 1.63 (0.65), residues: 58 loop : -1.31 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 635 HIS 0.003 0.001 HIS A 600 PHE 0.014 0.001 PHE A 769 TYR 0.039 0.001 TYR A 641 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 1106) hydrogen bonds : angle 3.61345 ( 3213) covalent geometry : bond 0.00320 (17034) covalent geometry : angle 0.55535 (23070) *********************** 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 216 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 1.699 Fit side-chains REVERT: A 346 GLU cc_start: 0.8889 (pm20) cc_final: 0.8673 (pm20) REVERT: A 578 MET cc_start: 0.8045 (mpp) cc_final: 0.7681 (mpp) REVERT: A 737 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 857 MET cc_start: 0.8522 (tmm) cc_final: 0.8078 (tmm) REVERT: A 967 MET cc_start: 0.8946 (mmm) cc_final: 0.8555 (mmm) REVERT: A 1104 MET cc_start: 0.8653 (mmp) cc_final: 0.8285 (mmp) REVERT: A 1107 MET cc_start: 0.7066 (tmm) cc_final: 0.6741 (ppp) REVERT: A 1172 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.6496 (m-70) REVERT: B 346 GLU cc_start: 0.8921 (pm20) cc_final: 0.8705 (pm20) REVERT: B 578 MET cc_start: 0.8000 (mpp) cc_final: 0.7628 (mpp) REVERT: B 967 MET cc_start: 0.8978 (mmm) cc_final: 0.8616 (mmm) REVERT: B 1107 MET cc_start: 0.6840 (tmm) cc_final: 0.6539 (tmm) REVERT: B 1169 ARG cc_start: 0.6850 (ttt180) cc_final: 0.6595 (ttt180) outliers start: 57 outliers final: 39 residues processed: 208 average time/residue: 0.2634 time to fit residues: 90.2229 Evaluate side-chains 197 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 322 SER Chi-restraints excluded: chain A residue 373 THR 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 644 LEU 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 850 VAL 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 1148 ILE Chi-restraints excluded: chain A residue 1172 HIS 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 321 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 644 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 157 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 75 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 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 = 0.3794 r_free = 0.3794 target = 0.108802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073769 restraints weight = 44680.477| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.53 r_work: 0.3010 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17034 Z= 0.111 Angle : 0.543 10.304 23070 Z= 0.270 Chirality : 0.038 0.190 2762 Planarity : 0.004 0.094 2828 Dihedral : 9.581 141.711 2345 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.21 % Allowed : 31.58 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 2086 helix: 2.70 (0.14), residues: 1372 sheet: 1.38 (0.63), residues: 62 loop : -1.28 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 635 HIS 0.004 0.000 HIS A 600 PHE 0.021 0.001 PHE B 769 TYR 0.025 0.001 TYR A 641 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 1106) hydrogen bonds : angle 3.52237 ( 3213) covalent geometry : bond 0.00237 (17034) covalent geometry : angle 0.54292 (23070) *********************** 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 202 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 2.958 Fit side-chains REVERT: A 224 LYS cc_start: 0.8958 (pptt) cc_final: 0.8718 (pptt) REVERT: A 578 MET cc_start: 0.8038 (mpp) cc_final: 0.7656 (mpp) REVERT: A 737 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: A 857 MET cc_start: 0.8499 (tmm) cc_final: 0.8039 (tmm) REVERT: A 967 MET cc_start: 0.8928 (mmm) cc_final: 0.8514 (mmm) REVERT: A 1104 MET cc_start: 0.8676 (mmp) cc_final: 0.8284 (mmp) REVERT: A 1107 MET cc_start: 0.7025 (tmm) cc_final: 0.6683 (ppp) REVERT: A 1172 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.6519 (m-70) REVERT: B 578 MET cc_start: 0.7990 (mpp) cc_final: 0.7615 (mpp) REVERT: B 967 MET cc_start: 0.8958 (mmm) cc_final: 0.8602 (mmm) REVERT: B 1107 MET cc_start: 0.6884 (tmm) cc_final: 0.6559 (tmm) outliers start: 40 outliers final: 33 residues processed: 194 average time/residue: 0.3018 time to fit residues: 94.1919 Evaluate side-chains 185 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 322 SER Chi-restraints excluded: chain A residue 373 THR 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 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 373 THR Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 677 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 187 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.107561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072368 restraints weight = 44604.839| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.46 r_work: 0.2987 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.133 Angle : 0.572 9.689 23070 Z= 0.285 Chirality : 0.038 0.164 2762 Planarity : 0.004 0.094 2828 Dihedral : 9.486 141.166 2345 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.49 % Allowed : 31.42 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 2086 helix: 2.72 (0.14), residues: 1370 sheet: 1.38 (0.63), residues: 62 loop : -1.31 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 635 HIS 0.002 0.000 HIS B 600 PHE 0.015 0.001 PHE A 699 TYR 0.021 0.001 TYR A 641 ARG 0.003 0.000 ARG B1158 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 1106) hydrogen bonds : angle 3.57407 ( 3213) covalent geometry : bond 0.00301 (17034) covalent geometry : angle 0.57201 (23070) *********************** 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 203 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 2.879 Fit side-chains REVERT: A 578 MET cc_start: 0.8019 (mpp) cc_final: 0.7603 (mpp) REVERT: A 737 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: A 857 MET cc_start: 0.8495 (tmm) cc_final: 0.8031 (tmm) REVERT: A 967 MET cc_start: 0.8928 (mmm) cc_final: 0.8512 (mmm) REVERT: A 1104 MET cc_start: 0.8691 (mmp) cc_final: 0.8322 (mmp) REVERT: A 1107 MET cc_start: 0.7019 (tmm) cc_final: 0.6681 (ppp) REVERT: A 1172 HIS cc_start: 0.6843 (OUTLIER) cc_final: 0.6500 (m-70) REVERT: B 578 MET cc_start: 0.7990 (mpp) cc_final: 0.7606 (mpp) REVERT: B 967 MET cc_start: 0.8961 (mmm) cc_final: 0.8600 (mmm) REVERT: B 1073 MET cc_start: 0.9039 (mmp) cc_final: 0.8667 (mmp) REVERT: B 1107 MET cc_start: 0.6852 (tmm) cc_final: 0.6548 (tmm) outliers start: 45 outliers final: 35 residues processed: 196 average time/residue: 0.2988 time to fit residues: 96.5660 Evaluate side-chains 189 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 322 SER Chi-restraints excluded: chain A residue 373 THR 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 1176 PHE 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 322 SER Chi-restraints excluded: chain B residue 373 THR 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 176 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.106270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070960 restraints weight = 44617.219| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.49 r_work: 0.2959 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17034 Z= 0.161 Angle : 0.605 9.179 23070 Z= 0.301 Chirality : 0.039 0.214 2762 Planarity : 0.004 0.094 2828 Dihedral : 9.453 142.025 2345 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.10 % Allowed : 32.08 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 2086 helix: 2.66 (0.14), residues: 1372 sheet: 1.67 (0.65), residues: 58 loop : -1.35 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 635 HIS 0.002 0.001 HIS A1120 PHE 0.021 0.001 PHE B 769 TYR 0.019 0.001 TYR A 641 ARG 0.004 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 1106) hydrogen bonds : angle 3.67501 ( 3213) covalent geometry : bond 0.00373 (17034) covalent geometry : angle 0.60528 (23070) ********************** 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 189 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.820 Fit side-chains REVERT: A 578 MET cc_start: 0.8048 (mpp) cc_final: 0.7630 (mpp) REVERT: A 857 MET cc_start: 0.8612 (tmm) cc_final: 0.8034 (tmm) REVERT: A 967 MET cc_start: 0.8919 (mmm) cc_final: 0.8507 (mmm) REVERT: A 1104 MET cc_start: 0.8754 (mmp) cc_final: 0.8374 (mmp) REVERT: A 1107 MET cc_start: 0.7109 (tmm) cc_final: 0.6793 (ppp) REVERT: A 1172 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6545 (m-70) REVERT: B 578 MET cc_start: 0.7945 (mpp) cc_final: 0.7593 (mpp) REVERT: B 967 MET cc_start: 0.8997 (mmm) cc_final: 0.8621 (mmm) REVERT: B 1107 MET cc_start: 0.6956 (tmm) cc_final: 0.6657 (tmm) outliers start: 38 outliers final: 35 residues processed: 182 average time/residue: 0.2679 time to fit residues: 78.9445 Evaluate side-chains 187 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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 322 SER Chi-restraints excluded: chain A residue 373 THR 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 817 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 1176 PHE 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 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 677 HIS 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 83 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 209 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.107837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072770 restraints weight = 44459.631| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.51 r_work: 0.2990 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.121 Angle : 0.578 9.205 23070 Z= 0.287 Chirality : 0.038 0.204 2762 Planarity : 0.004 0.094 2828 Dihedral : 9.381 142.522 2345 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 2.38 % Allowed : 31.69 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.19), residues: 2086 helix: 2.73 (0.14), residues: 1374 sheet: 1.42 (0.64), residues: 62 loop : -1.40 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 635 HIS 0.002 0.000 HIS B 600 PHE 0.019 0.001 PHE B 769 TYR 0.016 0.001 TYR A 641 ARG 0.006 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 1106) hydrogen bonds : angle 3.57235 ( 3213) covalent geometry : bond 0.00266 (17034) covalent geometry : angle 0.57823 (23070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9180.07 seconds wall clock time: 160 minutes 16.11 seconds (9616.11 seconds total)