Starting phenix.real_space_refine on Fri Jun 13 21:45:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f4n_28855/06_2025/8f4n_28855.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4n_28855/06_2025/8f4n_28855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f4n_28855/06_2025/8f4n_28855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4n_28855/06_2025/8f4n_28855.map" model { file = "/net/cci-nas-00/data/ceres_data/8f4n_28855/06_2025/8f4n_28855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4n_28855/06_2025/8f4n_28855.cif" } resolution = 2.95 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= 0.078 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 9954 2.51 5 N 2617 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15574 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7864 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 42, 'TRANS': 991} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7710 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 41, 'TRANS': 967} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 9.97, per 1000 atoms: 0.64 Number of scatterers: 15574 At special positions: 0 Unit cell: (79.18, 119.84, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 2915 8.00 N 2617 7.00 C 9954 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: 3.96 Conformation dependent library (CDL) restraints added in 2.1 seconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 61.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.588A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.761A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.613A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.647A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 316 removed outlier: 3.935A pdb=" N TYR B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 Proline residue: B 368 - end of helix removed outlier: 3.810A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.575A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.716A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 removed outlier: 4.228A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 459' Processing helix chain 'B' and resid 460 through 486 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.952A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 510 through 536 Processing helix chain 'B' and resid 536 through 558 removed outlier: 4.124A pdb=" N TRP B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 657 Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 782 through 786 removed outlier: 4.222A pdb=" N ASN B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 834 through 849 Processing helix chain 'B' and resid 859 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.529A pdb=" N PHE B 897 " --> pdb=" O TRP B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.613A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 3.872A pdb=" N ILE B 943 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 983 removed outlier: 5.108A pdb=" N ARG B 970 " --> pdb=" O ARG B 966 " (cutoff:3.500A) Proline residue: B 971 - end of helix removed outlier: 3.766A pdb=" N PHE B 979 " --> pdb=" O THR B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 988 Processing helix chain 'B' and resid 993 through 1030 removed outlier: 4.293A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Proline residue: B1020 - end of helix Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.906A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 99 through 118 removed outlier: 4.272A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.542A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.588A pdb=" N ASN A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.677A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 387 Proline residue: A 368 - end of helix removed outlier: 3.779A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 423 removed outlier: 3.724A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.569A pdb=" N GLY A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.559A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.324A pdb=" N MET A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 457' Processing helix chain 'A' and resid 460 through 496 removed outlier: 4.548A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.228A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 708 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.539A pdb=" N ILE A 784 " --> pdb=" O PRO A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 858 through 891 removed outlier: 3.614A pdb=" N GLN A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 918 removed outlier: 4.069A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 954 removed outlier: 4.549A pdb=" N PHE A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 988 removed outlier: 5.005A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix removed outlier: 3.633A pdb=" N PHE A 979 " --> pdb=" O THR A 975 " (cutoff:3.500A) Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.338A pdb=" N GLY A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.119A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N ARG B 813 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU B 824 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 815 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.119A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N ARG B 813 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU B 824 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 815 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER B 821 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.861A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.861A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 612 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.951A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA B 773 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER B 754 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 219 removed outlier: 3.869A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR B 233 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 727 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 235 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 729 " --> pdb=" O ASN B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 722 through 725 Processing sheet with id=AA8, first strand: chain 'B' and resid 728 through 729 Processing sheet with id=AA9, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AB1, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.999A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.415A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 828 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG A 713 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.999A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.415A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER A 821 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.639A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.639A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 623 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.431A pdb=" N TYR A 182 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 1116 hydrogen bonds defined for protein. 3270 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: 7.03 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5111 1.34 - 1.46: 2380 1.46 - 1.57: 8217 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 15876 Sorted by residual: bond pdb=" N GLY B 460 " pdb=" CA GLY B 460 " ideal model delta sigma weight residual 1.442 1.456 -0.014 7.70e-03 1.69e+04 3.31e+00 bond pdb=" CA ALA B 645 " pdb=" C ALA B 645 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.24e-02 6.50e+03 2.34e+00 bond pdb=" CA TYR A 467 " pdb=" C TYR A 467 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.27e-02 6.20e+03 1.96e+00 bond pdb=" CA LEU A 874 " pdb=" C LEU A 874 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.32e-02 5.74e+03 1.94e+00 bond pdb=" CA TYR A 157 " pdb=" C TYR A 157 " ideal model delta sigma weight residual 1.524 1.506 0.017 1.27e-02 6.20e+03 1.89e+00 ... (remaining 15871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 21147 1.57 - 3.14: 356 3.14 - 4.72: 54 4.72 - 6.29: 18 6.29 - 7.86: 5 Bond angle restraints: 21580 Sorted by residual: angle pdb=" C PHE B1030 " pdb=" N PRO B1031 " pdb=" CA PRO B1031 " ideal model delta sigma weight residual 120.03 116.51 3.52 9.90e-01 1.02e+00 1.26e+01 angle pdb=" CA LYS A1033 " pdb=" C LYS A1033 " pdb=" N PRO A1034 " ideal model delta sigma weight residual 120.77 117.49 3.28 9.70e-01 1.06e+00 1.14e+01 angle pdb=" CA LYS B1033 " pdb=" C LYS B1033 " pdb=" N PRO B1034 " ideal model delta sigma weight residual 120.77 117.57 3.20 9.70e-01 1.06e+00 1.09e+01 angle pdb=" C PHE A1030 " pdb=" N PRO A1031 " pdb=" CA PRO A1031 " ideal model delta sigma weight residual 119.85 116.61 3.24 1.01e+00 9.80e-01 1.03e+01 angle pdb=" N GLY A 147 " pdb=" CA GLY A 147 " pdb=" C GLY A 147 " ideal model delta sigma weight residual 115.43 110.94 4.49 1.41e+00 5.03e-01 1.01e+01 ... (remaining 21575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9097 17.97 - 35.94: 302 35.94 - 53.92: 55 53.92 - 71.89: 10 71.89 - 89.86: 6 Dihedral angle restraints: 9470 sinusoidal: 3602 harmonic: 5868 Sorted by residual: dihedral pdb=" CA ILE B 249 " pdb=" C ILE B 249 " pdb=" N THR B 250 " pdb=" CA THR B 250 " ideal model delta harmonic sigma weight residual 180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 156 " pdb=" CB ASP A 156 " pdb=" CG ASP A 156 " pdb=" OD1 ASP A 156 " ideal model delta sinusoidal sigma weight residual -30.00 -83.75 53.75 1 2.00e+01 2.50e-03 9.81e+00 dihedral pdb=" N LEU A 748 " pdb=" CA LEU A 748 " pdb=" CB LEU A 748 " pdb=" CG LEU A 748 " ideal model delta sinusoidal sigma weight residual -180.00 -121.55 -58.45 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 9467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1665 0.028 - 0.056: 552 0.056 - 0.084: 176 0.084 - 0.113: 110 0.113 - 0.141: 11 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA THR A 489 " pdb=" N THR A 489 " pdb=" C THR A 489 " pdb=" CB THR A 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2511 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 250 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C THR B 250 " -0.024 2.00e-02 2.50e+03 pdb=" O THR B 250 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 251 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 970 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO B 971 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 971 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 971 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 872 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" C PRO B 872 " -0.022 2.00e-02 2.50e+03 pdb=" O PRO B 872 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA B 873 " 0.007 2.00e-02 2.50e+03 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4209 2.80 - 3.33: 16030 3.33 - 3.85: 26593 3.85 - 4.38: 31118 4.38 - 4.90: 54008 Nonbonded interactions: 131958 Sorted by model distance: nonbonded pdb=" OD1 ASN A 415 " pdb=" NH1 ARG A 418 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU B 66 " pdb=" NH1 ARG B 816 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASN B 415 " pdb=" NH1 ARG B 418 " model vdw 2.284 3.120 nonbonded pdb=" OG1 THR A 46 " pdb=" OG1 THR A 128 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.294 3.040 ... (remaining 131953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 657 or (resid 658 and (name N or name CA or name \ C or name O or name CB )) or resid 659 through 731 or (resid 732 and (name N or \ name CA or name C or name O or name CB )) or resid 733 through 791 or (resid 79 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 793 through \ 1028 or (resid 1029 and (name N or name CA or name C or name O or name CB )) or \ resid 1030 through 1034)) selection = (chain 'B' and (resid 1 through 211 or resid 237 through 303 or (resid 304 and ( \ name N or name CA or name C or name O or name CB )) or resid 305 through 1034)) } 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: 29.980 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 40.350 Find NCS groups from input model: 0.740 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: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.004 0.037 15876 Z= 0.198 Angle : 0.547 7.861 21580 Z= 0.323 Chirality : 0.036 0.141 2514 Planarity : 0.003 0.033 2784 Dihedral : 9.959 89.860 5702 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.12 % Allowed : 4.60 % Favored : 93.28 % 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: 2.00 (0.19), residues: 2037 helix: 2.31 (0.15), residues: 1143 sheet: -0.36 (0.30), residues: 317 loop : 0.43 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.002 0.001 HIS B 600 PHE 0.009 0.001 PHE B 958 TYR 0.010 0.001 TYR B 157 ARG 0.002 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.15982 ( 1062) hydrogen bonds : angle 6.60320 ( 3270) covalent geometry : bond 0.00357 (15876) covalent geometry : angle 0.54718 (21580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 463 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 555 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6312 (t80) REVERT: B 920 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: A 151 LYS cc_start: 0.7573 (ttpm) cc_final: 0.7032 (tttp) REVERT: A 435 MET cc_start: 0.8107 (mmm) cc_final: 0.7848 (mmm) REVERT: A 897 PHE cc_start: 0.7353 (m-80) cc_final: 0.6915 (t80) outliers start: 35 outliers final: 6 residues processed: 487 average time/residue: 1.3080 time to fit residues: 701.0280 Evaluate side-chains 253 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 245 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 59 ASN B 63 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 108 GLN B 112 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 228 GLN B 237 GLN B 437 GLN B 439 GLN B 604 ASN B 684 GLN B 700 GLN B 724 GLN B 735 GLN B 870 GLN B 926 GLN B 967 GLN A 112 GLN A 360 GLN A 437 GLN A 439 GLN A 516 ASN A 517 GLN A 584 GLN A 691 HIS A 700 GLN A 716 HIS A 848 GLN A 870 GLN A 952 GLN A 955 HIS A 967 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104902 restraints weight = 18180.948| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.65 r_work: 0.3002 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15876 Z= 0.159 Angle : 0.554 8.115 21580 Z= 0.289 Chirality : 0.040 0.160 2514 Planarity : 0.004 0.034 2784 Dihedral : 4.486 57.911 2203 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.12 % Allowed : 14.04 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.19), residues: 2037 helix: 2.40 (0.15), residues: 1151 sheet: -0.18 (0.31), residues: 298 loop : 0.36 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 540 HIS 0.006 0.001 HIS A 955 PHE 0.019 0.001 PHE A 4 TYR 0.016 0.002 TYR A 182 ARG 0.005 0.001 ARG A 568 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 1062) hydrogen bonds : angle 4.98843 ( 3270) covalent geometry : bond 0.00359 (15876) covalent geometry : angle 0.55406 (21580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 1.724 Fit side-chains REVERT: B 68 ASN cc_start: 0.7654 (t0) cc_final: 0.7390 (t0) REVERT: B 115 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6713 (mtp) REVERT: B 152 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6535 (mt0) REVERT: B 170 ASN cc_start: 0.8224 (m110) cc_final: 0.7916 (t0) REVERT: B 267 THR cc_start: 0.8346 (p) cc_final: 0.8125 (p) REVERT: B 270 MET cc_start: 0.8619 (tpp) cc_final: 0.8404 (tpp) REVERT: B 456 MET cc_start: 0.8731 (mtm) cc_final: 0.8287 (mtm) REVERT: B 478 MET cc_start: 0.8677 (mmp) cc_final: 0.8233 (mmp) REVERT: B 496 LEU cc_start: 0.8577 (mt) cc_final: 0.8346 (mp) REVERT: B 522 ASN cc_start: 0.8361 (m-40) cc_final: 0.8088 (m110) REVERT: B 536 ARG cc_start: 0.6434 (mtm180) cc_final: 0.6091 (mtm180) REVERT: B 555 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6990 (t80) REVERT: B 588 LYS cc_start: 0.7906 (mptt) cc_final: 0.7363 (pttp) REVERT: B 652 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7550 (mtpt) REVERT: B 762 ASP cc_start: 0.8264 (t0) cc_final: 0.7954 (t0) REVERT: B 824 GLU cc_start: 0.8285 (tt0) cc_final: 0.7959 (tt0) REVERT: B 839 MET cc_start: 0.8952 (mtp) cc_final: 0.8539 (mtm) REVERT: B 920 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8459 (pt0) REVERT: B 945 GLU cc_start: 0.7820 (pp20) cc_final: 0.7600 (pp20) REVERT: A 115 MET cc_start: 0.8487 (tpp) cc_final: 0.7673 (mmt) REVERT: A 184 MET cc_start: 0.9026 (tpp) cc_final: 0.8590 (tpp) REVERT: A 244 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7375 (tm-30) REVERT: A 261 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7512 (mtt90) REVERT: A 363 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8069 (mtp85) REVERT: A 435 MET cc_start: 0.8624 (mmm) cc_final: 0.8254 (mmm) REVERT: A 478 MET cc_start: 0.8332 (mmm) cc_final: 0.7914 (mmp) REVERT: A 570 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8826 (ptt) REVERT: A 635 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: A 860 MET cc_start: 0.8326 (ttp) cc_final: 0.7637 (ttp) REVERT: A 953 LYS cc_start: 0.7266 (mmtp) cc_final: 0.6980 (mmtt) outliers start: 68 outliers final: 25 residues processed: 315 average time/residue: 1.3729 time to fit residues: 475.3265 Evaluate side-chains 267 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 155 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104604 restraints weight = 18226.520| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.64 r_work: 0.3005 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15876 Z= 0.139 Angle : 0.513 7.790 21580 Z= 0.264 Chirality : 0.039 0.181 2514 Planarity : 0.004 0.036 2784 Dihedral : 4.427 56.493 2201 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.48 % Allowed : 15.25 % Favored : 80.27 % 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: 1.99 (0.19), residues: 2037 helix: 2.31 (0.15), residues: 1155 sheet: -0.34 (0.30), residues: 306 loop : 0.33 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 540 HIS 0.002 0.001 HIS A 600 PHE 0.021 0.001 PHE A 4 TYR 0.015 0.001 TYR B 596 ARG 0.004 0.000 ARG B 966 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 1062) hydrogen bonds : angle 4.74406 ( 3270) covalent geometry : bond 0.00314 (15876) covalent geometry : angle 0.51316 (21580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 1.849 Fit side-chains REVERT: B 68 ASN cc_start: 0.7649 (t0) cc_final: 0.7340 (t0) REVERT: B 115 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6665 (mtp) REVERT: B 152 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6392 (mt0) REVERT: B 170 ASN cc_start: 0.8216 (m110) cc_final: 0.7950 (t0) REVERT: B 254 ASN cc_start: 0.7115 (m-40) cc_final: 0.6737 (m110) REVERT: B 267 THR cc_start: 0.8313 (p) cc_final: 0.8106 (p) REVERT: B 395 MET cc_start: 0.8870 (mmp) cc_final: 0.8640 (mmm) REVERT: B 414 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: B 456 MET cc_start: 0.8771 (mtm) cc_final: 0.8266 (mtm) REVERT: B 486 MET cc_start: 0.8506 (mtm) cc_final: 0.7970 (mmm) REVERT: B 496 LEU cc_start: 0.8578 (mt) cc_final: 0.8360 (mp) REVERT: B 518 MET cc_start: 0.8117 (ttp) cc_final: 0.7680 (tmm) REVERT: B 522 ASN cc_start: 0.8352 (m-40) cc_final: 0.7957 (m110) REVERT: B 524 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7409 (tp30) REVERT: B 536 ARG cc_start: 0.6582 (mtm180) cc_final: 0.6290 (mtm180) REVERT: B 555 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7050 (t80) REVERT: B 652 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7559 (mtpt) REVERT: B 748 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7281 (tp) REVERT: B 839 MET cc_start: 0.8951 (mtp) cc_final: 0.8648 (mtm) REVERT: B 860 MET cc_start: 0.7574 (ttp) cc_final: 0.7046 (tpp) REVERT: B 920 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: A 69 MET cc_start: 0.8464 (mmt) cc_final: 0.8046 (mmt) REVERT: A 76 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7176 (ttt) REVERT: A 322 GLU cc_start: 0.8007 (pt0) cc_final: 0.7776 (pt0) REVERT: A 435 MET cc_start: 0.8671 (mmm) cc_final: 0.8208 (mmm) REVERT: A 478 MET cc_start: 0.8356 (mmm) cc_final: 0.7906 (mmp) REVERT: A 518 MET cc_start: 0.7473 (ttp) cc_final: 0.7221 (ptt) REVERT: A 635 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: A 796 MET cc_start: 0.8502 (mmm) cc_final: 0.8056 (mtm) REVERT: A 824 GLU cc_start: 0.8995 (tt0) cc_final: 0.8686 (tp30) REVERT: A 860 MET cc_start: 0.8367 (ttp) cc_final: 0.7625 (ttp) REVERT: A 953 LYS cc_start: 0.7272 (mmtp) cc_final: 0.7013 (mmtt) outliers start: 74 outliers final: 34 residues processed: 289 average time/residue: 1.4465 time to fit residues: 458.0294 Evaluate side-chains 262 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 138 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 144 optimal weight: 0.0470 chunk 175 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 199 optimal weight: 0.0020 chunk 101 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 0.5086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 125 GLN ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107056 restraints weight = 18263.928| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.48 r_work: 0.3033 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15876 Z= 0.121 Angle : 0.499 7.405 21580 Z= 0.255 Chirality : 0.038 0.176 2514 Planarity : 0.004 0.041 2784 Dihedral : 4.370 55.237 2201 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.12 % Allowed : 16.10 % Favored : 79.78 % 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: 2.01 (0.19), residues: 2037 helix: 2.33 (0.15), residues: 1156 sheet: -0.27 (0.30), residues: 301 loop : 0.28 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 540 HIS 0.002 0.000 HIS A 600 PHE 0.017 0.001 PHE A 4 TYR 0.016 0.001 TYR B 596 ARG 0.005 0.000 ARG B 625 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 1062) hydrogen bonds : angle 4.59260 ( 3270) covalent geometry : bond 0.00262 (15876) covalent geometry : angle 0.49932 (21580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 2.044 Fit side-chains REVERT: B 68 ASN cc_start: 0.7598 (t0) cc_final: 0.7312 (t0) REVERT: B 115 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6728 (mtp) REVERT: B 152 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6546 (mt0) REVERT: B 170 ASN cc_start: 0.8223 (m110) cc_final: 0.8019 (t0) REVERT: B 254 ASN cc_start: 0.7131 (m-40) cc_final: 0.6780 (m110) REVERT: B 304 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: B 395 MET cc_start: 0.8889 (mmp) cc_final: 0.8686 (mmm) REVERT: B 414 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: B 456 MET cc_start: 0.8748 (mtm) cc_final: 0.8280 (mtm) REVERT: B 478 MET cc_start: 0.8721 (mmp) cc_final: 0.8375 (mmp) REVERT: B 486 MET cc_start: 0.8384 (mtm) cc_final: 0.8006 (mmm) REVERT: B 518 MET cc_start: 0.8169 (ttp) cc_final: 0.7764 (tmm) REVERT: B 522 ASN cc_start: 0.8435 (m-40) cc_final: 0.8039 (m110) REVERT: B 524 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7441 (tp30) REVERT: B 536 ARG cc_start: 0.6652 (mtm180) cc_final: 0.6339 (mtm180) REVERT: B 555 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 652 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7527 (mtpt) REVERT: B 717 ASN cc_start: 0.7672 (t0) cc_final: 0.7444 (t0) REVERT: B 748 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7408 (tp) REVERT: B 824 GLU cc_start: 0.8150 (tt0) cc_final: 0.7860 (tt0) REVERT: B 839 MET cc_start: 0.9006 (mtp) cc_final: 0.8787 (mtm) REVERT: B 860 MET cc_start: 0.7538 (ttp) cc_final: 0.7097 (tpp) REVERT: B 920 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: A 69 MET cc_start: 0.8520 (mmt) cc_final: 0.8031 (mmt) REVERT: A 76 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7332 (ttt) REVERT: A 322 GLU cc_start: 0.8019 (pt0) cc_final: 0.7790 (pt0) REVERT: A 435 MET cc_start: 0.8695 (mmm) cc_final: 0.8429 (mmm) REVERT: A 635 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: A 715 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7777 (ptp-170) REVERT: A 763 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7718 (mtm110) REVERT: A 796 MET cc_start: 0.8525 (mmm) cc_final: 0.8075 (mtm) REVERT: A 824 GLU cc_start: 0.8962 (tt0) cc_final: 0.8656 (tp30) REVERT: A 860 MET cc_start: 0.8404 (ttp) cc_final: 0.7695 (ttp) REVERT: A 953 LYS cc_start: 0.7209 (mmtp) cc_final: 0.6978 (mmtt) outliers start: 68 outliers final: 31 residues processed: 281 average time/residue: 1.4435 time to fit residues: 446.4158 Evaluate side-chains 264 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 165 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN A 745 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105474 restraints weight = 18540.480| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.49 r_work: 0.3017 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15876 Z= 0.140 Angle : 0.516 8.578 21580 Z= 0.262 Chirality : 0.039 0.159 2514 Planarity : 0.004 0.044 2784 Dihedral : 4.393 54.575 2201 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.60 % Allowed : 16.46 % Favored : 78.93 % 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: 1.98 (0.19), residues: 2037 helix: 2.31 (0.15), residues: 1155 sheet: -0.28 (0.30), residues: 303 loop : 0.29 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.002 0.001 HIS A 600 PHE 0.018 0.001 PHE B 958 TYR 0.017 0.001 TYR B 596 ARG 0.004 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 1062) hydrogen bonds : angle 4.57672 ( 3270) covalent geometry : bond 0.00326 (15876) covalent geometry : angle 0.51635 (21580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 235 time to evaluate : 1.824 Fit side-chains REVERT: B 68 ASN cc_start: 0.7518 (t0) cc_final: 0.7201 (t0) REVERT: B 346 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: B 414 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: B 456 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8282 (mtm) REVERT: B 478 MET cc_start: 0.8682 (mmp) cc_final: 0.8319 (mmp) REVERT: B 486 MET cc_start: 0.8329 (mtm) cc_final: 0.7969 (mmm) REVERT: B 522 ASN cc_start: 0.8478 (m-40) cc_final: 0.8174 (m110) REVERT: B 524 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7444 (tp30) REVERT: B 536 ARG cc_start: 0.6706 (mtm180) cc_final: 0.6491 (mtm180) REVERT: B 555 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7164 (t80) REVERT: B 603 ASP cc_start: 0.8335 (m-30) cc_final: 0.8112 (m-30) REVERT: B 652 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7555 (mtpt) REVERT: B 717 ASN cc_start: 0.7703 (t0) cc_final: 0.7499 (t0) REVERT: B 748 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7421 (tp) REVERT: B 824 GLU cc_start: 0.8268 (tt0) cc_final: 0.7878 (tt0) REVERT: B 860 MET cc_start: 0.7587 (ttp) cc_final: 0.7141 (tpp) REVERT: B 920 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: A 69 MET cc_start: 0.8484 (mmt) cc_final: 0.8023 (mmt) REVERT: A 76 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7344 (ttt) REVERT: A 322 GLU cc_start: 0.8048 (pt0) cc_final: 0.7833 (pt0) REVERT: A 342 LYS cc_start: 0.8279 (tttp) cc_final: 0.8012 (tttm) REVERT: A 435 MET cc_start: 0.8738 (mmm) cc_final: 0.8449 (mmm) REVERT: A 625 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8147 (ttp-170) REVERT: A 635 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: A 715 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7777 (ptp-170) REVERT: A 763 ARG cc_start: 0.8177 (mtm110) cc_final: 0.7688 (mtm110) REVERT: A 796 MET cc_start: 0.8610 (mmm) cc_final: 0.8142 (mtm) REVERT: A 860 MET cc_start: 0.8407 (ttp) cc_final: 0.7698 (ttp) REVERT: A 953 LYS cc_start: 0.7243 (mmtp) cc_final: 0.7020 (mmtt) outliers start: 76 outliers final: 35 residues processed: 275 average time/residue: 1.4391 time to fit residues: 437.3595 Evaluate side-chains 267 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 16 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 166 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 125 GLN B 724 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106186 restraints weight = 18359.628| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.49 r_work: 0.3032 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15876 Z= 0.125 Angle : 0.503 7.580 21580 Z= 0.255 Chirality : 0.038 0.154 2514 Planarity : 0.004 0.043 2784 Dihedral : 4.356 53.672 2201 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.12 % Allowed : 17.13 % Favored : 78.75 % 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: 2.01 (0.19), residues: 2037 helix: 2.34 (0.15), residues: 1152 sheet: -0.21 (0.30), residues: 309 loop : 0.25 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 540 HIS 0.002 0.001 HIS A 600 PHE 0.015 0.001 PHE B 958 TYR 0.017 0.001 TYR B 596 ARG 0.004 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 1062) hydrogen bonds : angle 4.52788 ( 3270) covalent geometry : bond 0.00280 (15876) covalent geometry : angle 0.50323 (21580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 1.700 Fit side-chains REVERT: B 67 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: B 68 ASN cc_start: 0.7513 (t0) cc_final: 0.7202 (t0) REVERT: B 81 GLN cc_start: 0.7808 (mp10) cc_final: 0.7478 (pm20) REVERT: B 304 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: B 353 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8355 (mt) REVERT: B 404 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7876 (mt) REVERT: B 414 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: B 435 MET cc_start: 0.8514 (mmm) cc_final: 0.8202 (mmp) REVERT: B 456 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8310 (mtm) REVERT: B 478 MET cc_start: 0.8638 (mmp) cc_final: 0.8297 (mmp) REVERT: B 486 MET cc_start: 0.8296 (mtm) cc_final: 0.7978 (mmm) REVERT: B 522 ASN cc_start: 0.8399 (m-40) cc_final: 0.8080 (m110) REVERT: B 524 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7434 (tp30) REVERT: B 536 ARG cc_start: 0.6684 (mtm180) cc_final: 0.6478 (mtm180) REVERT: B 555 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 603 ASP cc_start: 0.8336 (m-30) cc_final: 0.8124 (m-30) REVERT: B 652 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7538 (mtpt) REVERT: B 748 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7419 (tp) REVERT: B 772 GLN cc_start: 0.7869 (mt0) cc_final: 0.7634 (mp10) REVERT: B 824 GLU cc_start: 0.8122 (tt0) cc_final: 0.7821 (tt0) REVERT: B 860 MET cc_start: 0.7596 (ttp) cc_final: 0.7142 (tpp) REVERT: B 920 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: A 69 MET cc_start: 0.8466 (mmt) cc_final: 0.7912 (mmt) REVERT: A 76 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7358 (ttt) REVERT: A 241 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7763 (mm110) REVERT: A 342 LYS cc_start: 0.8269 (tttp) cc_final: 0.8004 (tttm) REVERT: A 525 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6739 (ttp-170) REVERT: A 625 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8140 (ttp-170) REVERT: A 635 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: A 656 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7727 (mt0) REVERT: A 715 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7791 (ptp-170) REVERT: A 763 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7902 (mtm110) REVERT: A 796 MET cc_start: 0.8607 (mmm) cc_final: 0.8117 (mtm) REVERT: A 824 GLU cc_start: 0.8831 (tt0) cc_final: 0.8485 (tp30) REVERT: A 860 MET cc_start: 0.8399 (ttp) cc_final: 0.7678 (ttp) REVERT: A 953 LYS cc_start: 0.7219 (mmtp) cc_final: 0.7008 (mmtt) outliers start: 68 outliers final: 33 residues processed: 273 average time/residue: 1.3890 time to fit residues: 415.8701 Evaluate side-chains 269 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 51 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 684 GLN ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105856 restraints weight = 18304.942| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.48 r_work: 0.3014 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15876 Z= 0.135 Angle : 0.511 7.636 21580 Z= 0.260 Chirality : 0.039 0.156 2514 Planarity : 0.004 0.044 2784 Dihedral : 4.374 52.781 2201 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.87 % Allowed : 17.37 % Favored : 78.75 % 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: 2.00 (0.19), residues: 2037 helix: 2.33 (0.15), residues: 1151 sheet: -0.22 (0.31), residues: 305 loop : 0.25 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 540 HIS 0.002 0.001 HIS A 600 PHE 0.015 0.001 PHE B 958 TYR 0.019 0.001 TYR B 596 ARG 0.006 0.000 ARG A 816 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 1062) hydrogen bonds : angle 4.51809 ( 3270) covalent geometry : bond 0.00310 (15876) covalent geometry : angle 0.51058 (21580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 1.689 Fit side-chains REVERT: B 59 ASN cc_start: 0.7298 (m110) cc_final: 0.6931 (m110) REVERT: B 68 ASN cc_start: 0.7485 (t0) cc_final: 0.7190 (t0) REVERT: B 152 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6329 (mt0) REVERT: B 304 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: B 414 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: B 435 MET cc_start: 0.8484 (mmm) cc_final: 0.8070 (mmp) REVERT: B 456 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: B 486 MET cc_start: 0.8252 (mtm) cc_final: 0.7885 (mmm) REVERT: B 522 ASN cc_start: 0.8303 (m-40) cc_final: 0.7989 (m110) REVERT: B 524 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7383 (tp30) REVERT: B 536 ARG cc_start: 0.6430 (mtm180) cc_final: 0.6088 (mtm180) REVERT: B 588 LYS cc_start: 0.7831 (mmpt) cc_final: 0.7373 (pttp) REVERT: B 603 ASP cc_start: 0.8320 (m-30) cc_final: 0.8100 (m-30) REVERT: B 652 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7473 (mtpt) REVERT: B 772 GLN cc_start: 0.7837 (mt0) cc_final: 0.7597 (mp10) REVERT: B 824 GLU cc_start: 0.8119 (tt0) cc_final: 0.7815 (tt0) REVERT: B 860 MET cc_start: 0.7547 (ttp) cc_final: 0.7021 (tpp) REVERT: B 920 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: A 69 MET cc_start: 0.8359 (mmt) cc_final: 0.7733 (mmt) REVERT: A 76 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7210 (ttt) REVERT: A 342 LYS cc_start: 0.8199 (tttp) cc_final: 0.7861 (tttm) REVERT: A 525 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6661 (ttp-170) REVERT: A 625 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8182 (ttp-170) REVERT: A 635 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: A 656 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7694 (mp10) REVERT: A 715 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7701 (ptp-170) REVERT: A 763 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7837 (mtm110) REVERT: A 796 MET cc_start: 0.8665 (mmm) cc_final: 0.8164 (mtm) REVERT: A 824 GLU cc_start: 0.8837 (tt0) cc_final: 0.8437 (tp30) REVERT: A 860 MET cc_start: 0.8330 (ttp) cc_final: 0.7584 (ttp) REVERT: A 891 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: A 953 LYS cc_start: 0.7229 (mmtp) cc_final: 0.7019 (mmtt) outliers start: 64 outliers final: 34 residues processed: 263 average time/residue: 1.5019 time to fit residues: 433.1055 Evaluate side-chains 269 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 1013 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 171 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 655 ASN ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105611 restraints weight = 18237.787| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.49 r_work: 0.3015 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15876 Z= 0.135 Angle : 0.515 7.897 21580 Z= 0.262 Chirality : 0.039 0.155 2514 Planarity : 0.004 0.042 2784 Dihedral : 4.227 49.862 2199 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.51 % Allowed : 18.16 % Favored : 78.33 % 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: 1.99 (0.19), residues: 2037 helix: 2.33 (0.15), residues: 1150 sheet: -0.22 (0.31), residues: 305 loop : 0.24 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.002 0.001 HIS B 319 PHE 0.014 0.001 PHE B 958 TYR 0.018 0.001 TYR B 596 ARG 0.007 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1062) hydrogen bonds : angle 4.50840 ( 3270) covalent geometry : bond 0.00311 (15876) covalent geometry : angle 0.51474 (21580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 1.749 Fit side-chains REVERT: B 59 ASN cc_start: 0.7223 (m110) cc_final: 0.6981 (m110) REVERT: B 68 ASN cc_start: 0.7569 (t0) cc_final: 0.7299 (t0) REVERT: B 125 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6371 (tp40) REVERT: B 152 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6476 (mt0) REVERT: B 304 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: B 414 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: B 435 MET cc_start: 0.8442 (mmm) cc_final: 0.8152 (mmp) REVERT: B 456 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8341 (mtm) REVERT: B 478 MET cc_start: 0.8699 (mmp) cc_final: 0.8394 (mmp) REVERT: B 486 MET cc_start: 0.8255 (mtm) cc_final: 0.7903 (mmm) REVERT: B 522 ASN cc_start: 0.8318 (m-40) cc_final: 0.8015 (m110) REVERT: B 524 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7399 (tp30) REVERT: B 536 ARG cc_start: 0.6406 (mtm180) cc_final: 0.6076 (mtm180) REVERT: B 588 LYS cc_start: 0.7828 (mmpt) cc_final: 0.7379 (pttp) REVERT: B 603 ASP cc_start: 0.8319 (m-30) cc_final: 0.8104 (m-30) REVERT: B 652 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7512 (mtpt) REVERT: B 772 GLN cc_start: 0.7840 (mt0) cc_final: 0.7613 (mp10) REVERT: B 824 GLU cc_start: 0.8133 (tt0) cc_final: 0.7823 (tt0) REVERT: B 860 MET cc_start: 0.7549 (ttp) cc_final: 0.7012 (tpp) REVERT: A 69 MET cc_start: 0.8355 (mmt) cc_final: 0.7694 (mmt) REVERT: A 76 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7207 (ttt) REVERT: A 342 LYS cc_start: 0.8203 (tttp) cc_final: 0.7886 (tttm) REVERT: A 525 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6657 (ttp-170) REVERT: A 625 ARG cc_start: 0.8410 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: A 635 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 656 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7705 (mp10) REVERT: A 715 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7712 (ptp-170) REVERT: A 763 ARG cc_start: 0.8207 (mtm110) cc_final: 0.7907 (mtm110) REVERT: A 796 MET cc_start: 0.8705 (mmm) cc_final: 0.8177 (mtm) REVERT: A 824 GLU cc_start: 0.8790 (tt0) cc_final: 0.8422 (tp30) REVERT: A 860 MET cc_start: 0.8336 (ttp) cc_final: 0.7581 (ttp) REVERT: A 891 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: A 953 LYS cc_start: 0.7175 (mmtp) cc_final: 0.6960 (mmtt) REVERT: A 970 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8121 (tmm-80) outliers start: 58 outliers final: 29 residues processed: 258 average time/residue: 1.4890 time to fit residues: 421.3615 Evaluate side-chains 260 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 970 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 86 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 167 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 360 GLN A 516 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.130198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105188 restraints weight = 18326.942| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.49 r_work: 0.3009 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15876 Z= 0.142 Angle : 0.527 7.791 21580 Z= 0.269 Chirality : 0.039 0.156 2514 Planarity : 0.004 0.041 2784 Dihedral : 4.262 50.552 2199 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.15 % Allowed : 18.34 % Favored : 78.51 % 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: 1.93 (0.19), residues: 2037 helix: 2.27 (0.15), residues: 1151 sheet: -0.27 (0.31), residues: 302 loop : 0.22 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 540 HIS 0.002 0.001 HIS B 686 PHE 0.013 0.001 PHE B 958 TYR 0.020 0.001 TYR B 596 ARG 0.008 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 1062) hydrogen bonds : angle 4.52749 ( 3270) covalent geometry : bond 0.00331 (15876) covalent geometry : angle 0.52729 (21580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 1.710 Fit side-chains REVERT: B 55 GLN cc_start: 0.7678 (tp40) cc_final: 0.7265 (tp-100) REVERT: B 59 ASN cc_start: 0.7180 (m110) cc_final: 0.6691 (m110) REVERT: B 125 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6366 (tp40) REVERT: B 152 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6490 (mt0) REVERT: B 304 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: B 414 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: B 435 MET cc_start: 0.8432 (mmm) cc_final: 0.8093 (mmp) REVERT: B 456 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: B 478 MET cc_start: 0.8668 (mmp) cc_final: 0.8320 (mmp) REVERT: B 486 MET cc_start: 0.8269 (mtm) cc_final: 0.7916 (mmm) REVERT: B 522 ASN cc_start: 0.8318 (m-40) cc_final: 0.8015 (m110) REVERT: B 524 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7409 (tp30) REVERT: B 536 ARG cc_start: 0.6352 (mtm180) cc_final: 0.6034 (mtm180) REVERT: B 588 LYS cc_start: 0.7832 (mmpt) cc_final: 0.7389 (pttp) REVERT: B 603 ASP cc_start: 0.8322 (m-30) cc_final: 0.8111 (m-30) REVERT: B 652 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7508 (mtpt) REVERT: B 772 GLN cc_start: 0.7842 (mt0) cc_final: 0.7617 (mp10) REVERT: B 824 GLU cc_start: 0.8151 (tt0) cc_final: 0.7834 (tt0) REVERT: B 860 MET cc_start: 0.7597 (ttp) cc_final: 0.7032 (tpp) REVERT: A 69 MET cc_start: 0.8346 (mmt) cc_final: 0.7701 (mmt) REVERT: A 76 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7207 (ttt) REVERT: A 342 LYS cc_start: 0.8221 (tttp) cc_final: 0.7883 (tttm) REVERT: A 525 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6629 (ttp-170) REVERT: A 625 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: A 635 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: A 656 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7648 (mp10) REVERT: A 715 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7710 (ptp-170) REVERT: A 763 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7902 (mtm110) REVERT: A 796 MET cc_start: 0.8719 (mmm) cc_final: 0.8160 (mtm) REVERT: A 824 GLU cc_start: 0.8789 (tt0) cc_final: 0.8434 (tp30) REVERT: A 860 MET cc_start: 0.8344 (ttp) cc_final: 0.7593 (ttp) REVERT: A 891 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: A 953 LYS cc_start: 0.7199 (mmtp) cc_final: 0.6985 (mmtt) REVERT: A 970 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7797 (ttt180) outliers start: 52 outliers final: 29 residues processed: 252 average time/residue: 1.5174 time to fit residues: 418.8152 Evaluate side-chains 261 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 970 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 123 GLN A 516 ASN A 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.129703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104717 restraints weight = 18448.005| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.49 r_work: 0.3002 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15876 Z= 0.148 Angle : 0.532 7.935 21580 Z= 0.270 Chirality : 0.039 0.156 2514 Planarity : 0.004 0.042 2784 Dihedral : 4.301 51.427 2199 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.78 % Allowed : 18.77 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.19), residues: 2037 helix: 2.23 (0.15), residues: 1151 sheet: -0.36 (0.30), residues: 309 loop : 0.21 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.002 0.001 HIS B 319 PHE 0.012 0.001 PHE B 958 TYR 0.021 0.001 TYR B 596 ARG 0.007 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 1062) hydrogen bonds : angle 4.54224 ( 3270) covalent geometry : bond 0.00348 (15876) covalent geometry : angle 0.53173 (21580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 1.673 Fit side-chains REVERT: B 59 ASN cc_start: 0.7159 (m110) cc_final: 0.6844 (m110) REVERT: B 67 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7600 (mp-120) REVERT: B 125 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6394 (tp40) REVERT: B 152 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6485 (mt0) REVERT: B 254 ASN cc_start: 0.7181 (m-40) cc_final: 0.6806 (m110) REVERT: B 304 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: B 414 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: B 435 MET cc_start: 0.8395 (mmm) cc_final: 0.8073 (mmp) REVERT: B 456 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8308 (mtm) REVERT: B 478 MET cc_start: 0.8678 (mmp) cc_final: 0.8338 (mmp) REVERT: B 486 MET cc_start: 0.8273 (mtm) cc_final: 0.7917 (mmm) REVERT: B 518 MET cc_start: 0.8104 (tmm) cc_final: 0.7721 (tmm) REVERT: B 522 ASN cc_start: 0.8340 (m-40) cc_final: 0.7910 (m110) REVERT: B 524 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7406 (tp30) REVERT: B 536 ARG cc_start: 0.6390 (mtm180) cc_final: 0.6077 (mtm180) REVERT: B 588 LYS cc_start: 0.7842 (mmpt) cc_final: 0.7413 (pttp) REVERT: B 594 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7710 (mt-10) REVERT: B 652 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7518 (mtpt) REVERT: B 824 GLU cc_start: 0.8152 (tt0) cc_final: 0.7806 (tt0) REVERT: B 860 MET cc_start: 0.7509 (ttp) cc_final: 0.7070 (tpp) REVERT: A 69 MET cc_start: 0.8343 (mmt) cc_final: 0.7718 (mmt) REVERT: A 342 LYS cc_start: 0.8238 (tttp) cc_final: 0.7892 (tttm) REVERT: A 525 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6661 (ttp-170) REVERT: A 625 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: A 635 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: A 656 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7653 (mp10) REVERT: A 715 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7709 (ptp-170) REVERT: A 763 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7866 (mtm110) REVERT: A 796 MET cc_start: 0.8708 (mmm) cc_final: 0.8140 (mtm) REVERT: A 824 GLU cc_start: 0.8786 (tt0) cc_final: 0.8450 (tp30) REVERT: A 860 MET cc_start: 0.8343 (ttp) cc_final: 0.7592 (ttp) REVERT: A 891 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: A 953 LYS cc_start: 0.7213 (mmtp) cc_final: 0.6993 (mmtt) REVERT: A 970 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7871 (ttt180) outliers start: 46 outliers final: 30 residues processed: 248 average time/residue: 1.4636 time to fit residues: 400.9632 Evaluate side-chains 259 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 970 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 201 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 165 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN B 772 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.106162 restraints weight = 18257.484| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.49 r_work: 0.3023 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15876 Z= 0.126 Angle : 0.517 7.646 21580 Z= 0.262 Chirality : 0.039 0.160 2514 Planarity : 0.004 0.041 2784 Dihedral : 4.274 51.366 2199 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.72 % Allowed : 19.07 % Favored : 78.21 % 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: 1.90 (0.19), residues: 2037 helix: 2.27 (0.15), residues: 1151 sheet: -0.28 (0.31), residues: 299 loop : 0.16 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 540 HIS 0.002 0.001 HIS B 686 PHE 0.011 0.001 PHE B 958 TYR 0.022 0.001 TYR B 596 ARG 0.005 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 1062) hydrogen bonds : angle 4.49547 ( 3270) covalent geometry : bond 0.00286 (15876) covalent geometry : angle 0.51654 (21580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12125.48 seconds wall clock time: 209 minutes 31.61 seconds (12571.61 seconds total)