Starting phenix.real_space_refine on Mon Nov 18 04:26:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/11_2024/8f4n_28855.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/11_2024/8f4n_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/11_2024/8f4n_28855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/11_2024/8f4n_28855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/11_2024/8f4n_28855.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/11_2024/8f4n_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-5513/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: 9.92, 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: 3.92 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: 1.96 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: 7.04 Time building geometry restraints manager: 4.56 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: 2.500 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.350 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.790 ------------------------------------------------------------------------------- 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= 0.238 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 *********************** 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 : 1.709 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: 1.3535 time to fit residues: 726.3896 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 : 1.815 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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= 0.242 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 *********************** 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 : 1.697 Fit side-chains REVERT: B 115 MET cc_start: 0.5263 (OUTLIER) cc_final: 0.5062 (mtp) REVERT: B 152 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.5970 (mt0) REVERT: B 456 MET cc_start: 0.8278 (mtm) cc_final: 0.7827 (mtm) REVERT: B 478 MET cc_start: 0.8080 (mmp) cc_final: 0.7650 (mmp) REVERT: B 516 ASN cc_start: 0.8015 (m-40) cc_final: 0.7807 (m110) REVERT: B 555 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6513 (t80) REVERT: B 652 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7400 (mtpt) REVERT: B 839 MET cc_start: 0.8788 (mtp) cc_final: 0.8416 (mtm) REVERT: B 920 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: A 115 MET cc_start: 0.7390 (tpp) cc_final: 0.7071 (mmt) REVERT: A 184 MET cc_start: 0.8190 (tpp) cc_final: 0.7785 (tpp) REVERT: A 261 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6699 (mtt90) REVERT: A 435 MET cc_start: 0.8110 (mmm) cc_final: 0.7794 (mmm) REVERT: A 478 MET cc_start: 0.8208 (mmm) cc_final: 0.7830 (mmp) REVERT: A 635 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: A 659 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6973 (mt-10) outliers start: 68 outliers final: 25 residues processed: 315 average time/residue: 1.3972 time to fit residues: 483.3991 Evaluate side-chains 263 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 452 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 659 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 102 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 184 optimal weight: 0.8980 chunk 199 optimal weight: 0.0870 chunk 164 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 684 GLN B 724 GLN B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15876 Z= 0.275 Angle : 0.545 8.010 21580 Z= 0.282 Chirality : 0.040 0.186 2514 Planarity : 0.004 0.039 2784 Dihedral : 4.520 57.006 2201 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.96 % Allowed : 14.77 % 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: 1.87 (0.19), residues: 2037 helix: 2.18 (0.15), residues: 1157 sheet: -0.34 (0.30), residues: 303 loop : 0.30 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.003 0.001 HIS B 319 PHE 0.020 0.001 PHE A 4 TYR 0.015 0.002 TYR B 596 ARG 0.004 0.001 ARG B 539 *********************** 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 315 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 233 time to evaluate : 2.036 Fit side-chains REVERT: B 152 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.5859 (mt0) REVERT: B 395 MET cc_start: 0.8363 (mmp) cc_final: 0.8132 (mmm) REVERT: B 456 MET cc_start: 0.8376 (mtm) cc_final: 0.7892 (mtm) REVERT: B 478 MET cc_start: 0.8182 (mmp) cc_final: 0.7926 (mmp) REVERT: B 555 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6515 (t80) REVERT: B 652 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7509 (mtpt) REVERT: B 839 MET cc_start: 0.8778 (mtp) cc_final: 0.8528 (mtm) REVERT: B 920 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: A 69 MET cc_start: 0.8181 (mmt) cc_final: 0.7756 (mmt) REVERT: A 76 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7530 (ttt) REVERT: A 435 MET cc_start: 0.8135 (mmm) cc_final: 0.7882 (mmm) REVERT: A 478 MET cc_start: 0.8326 (mmm) cc_final: 0.7835 (mmp) REVERT: A 525 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6717 (ttp-170) REVERT: A 635 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6673 (mt-10) REVERT: A 796 MET cc_start: 0.7515 (mmm) cc_final: 0.7312 (mtm) outliers start: 82 outliers final: 40 residues processed: 279 average time/residue: 1.4625 time to fit residues: 447.1700 Evaluate side-chains 265 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE 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 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 167 SER Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 125 GLN B 522 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 55 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN A 360 GLN A 745 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15876 Z= 0.228 Angle : 0.524 7.951 21580 Z= 0.269 Chirality : 0.039 0.163 2514 Planarity : 0.004 0.039 2784 Dihedral : 4.502 55.639 2201 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.66 % Allowed : 15.01 % Favored : 80.33 % 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: 1.86 (0.19), residues: 2037 helix: 2.21 (0.15), residues: 1151 sheet: -0.31 (0.31), residues: 296 loop : 0.22 (0.27), residues: 590 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 0.017 0.001 PHE A 4 TYR 0.017 0.001 TYR B 596 ARG 0.005 0.000 ARG B 539 *********************** 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 310 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 233 time to evaluate : 1.696 Fit side-chains REVERT: B 152 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.5995 (mt0) REVERT: B 304 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6033 (tp30) REVERT: B 555 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6549 (t80) REVERT: B 652 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7434 (mtpt) REVERT: A 76 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7569 (ttt) REVERT: A 435 MET cc_start: 0.8137 (mmm) cc_final: 0.7912 (mmm) REVERT: A 635 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: A 763 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7150 (mtm110) outliers start: 77 outliers final: 40 residues processed: 277 average time/residue: 1.4433 time to fit residues: 438.2814 Evaluate side-chains 259 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 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 265 VAL Chi-restraints excluded: chain B residue 304 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 573 THR 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 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 164 ASP Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 270 MET 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 545 VAL Chi-restraints excluded: chain A residue 573 THR 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 851 ASN 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 163 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 167 optimal weight: 0.0870 chunk 135 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 516 ASN ** 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 516 ASN A 517 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15876 Z= 0.190 Angle : 0.509 7.590 21580 Z= 0.260 Chirality : 0.039 0.184 2514 Planarity : 0.004 0.040 2784 Dihedral : 4.439 54.550 2201 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.00 % Allowed : 16.89 % Favored : 79.12 % 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: 1.91 (0.19), residues: 2037 helix: 2.25 (0.15), residues: 1153 sheet: -0.27 (0.31), residues: 297 loop : 0.20 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 540 HIS 0.003 0.001 HIS B 955 PHE 0.022 0.001 PHE B 958 TYR 0.017 0.001 TYR B 596 ARG 0.006 0.000 ARG B 625 *********************** 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 294 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 228 time to evaluate : 1.822 Fit side-chains REVERT: B 152 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.5967 (mt0) REVERT: B 304 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6027 (tp30) REVERT: B 435 MET cc_start: 0.7851 (mmm) cc_final: 0.7592 (mmp) REVERT: B 478 MET cc_start: 0.8132 (mmp) cc_final: 0.7770 (mmp) REVERT: B 536 ARG cc_start: 0.6708 (mtm180) cc_final: 0.6388 (ptt180) REVERT: B 555 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6603 (t80) REVERT: B 652 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7369 (mtpt) REVERT: A 62 THR cc_start: 0.8319 (m) cc_final: 0.8080 (m) REVERT: A 76 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7584 (ttt) REVERT: A 635 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: A 715 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7772 (ptp-170) REVERT: A 763 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7153 (mtm110) outliers start: 66 outliers final: 37 residues processed: 267 average time/residue: 1.3840 time to fit residues: 406.9633 Evaluate side-chains 259 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 SER 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 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 452 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR 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 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 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 626 MET 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 715 ARG Chi-restraints excluded: chain A residue 742 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 B 731 GLN B 735 GLN ** B 772 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15876 Z= 0.261 Angle : 0.541 8.563 21580 Z= 0.275 Chirality : 0.040 0.160 2514 Planarity : 0.004 0.044 2784 Dihedral : 4.518 54.006 2201 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.48 % Allowed : 17.01 % 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: 1.80 (0.19), residues: 2037 helix: 2.15 (0.15), residues: 1151 sheet: -0.26 (0.31), residues: 293 loop : 0.14 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.004 0.001 HIS B 955 PHE 0.016 0.001 PHE B 958 TYR 0.020 0.001 TYR B 596 ARG 0.005 0.000 ARG B 539 *********************** 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 305 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 231 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: B 304 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6049 (tp30) REVERT: B 435 MET cc_start: 0.7904 (mmm) cc_final: 0.7678 (mmp) REVERT: B 478 MET cc_start: 0.8159 (mmp) cc_final: 0.7911 (mmp) REVERT: B 536 ARG cc_start: 0.6641 (mtm180) cc_final: 0.6438 (ptt180) REVERT: B 555 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6625 (t80) REVERT: B 652 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7442 (mtpt) REVERT: A 62 THR cc_start: 0.8514 (m) cc_final: 0.8302 (m) REVERT: A 625 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7566 (ttp-170) REVERT: A 635 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: A 715 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7694 (ptp-170) REVERT: A 763 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7181 (mtm110) outliers start: 74 outliers final: 41 residues processed: 269 average time/residue: 1.5077 time to fit residues: 445.0432 Evaluate side-chains 259 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 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 355 MET 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 573 THR 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 692 ASP Chi-restraints excluded: chain B residue 731 GLN 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 A residue 24 THR Chi-restraints excluded: chain A residue 164 ASP 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 528 LYS 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 663 ILE 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 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 1013 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 chunk 165 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 686 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3167 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= 0.201 Angle : 0.519 8.104 21580 Z= 0.264 Chirality : 0.039 0.156 2514 Planarity : 0.004 0.043 2784 Dihedral : 4.474 52.741 2201 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.33 % Allowed : 18.40 % Favored : 78.27 % 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: 1.83 (0.19), residues: 2037 helix: 2.21 (0.15), residues: 1151 sheet: -0.29 (0.31), residues: 286 loop : 0.12 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 540 HIS 0.004 0.001 HIS B 955 PHE 0.014 0.001 PHE B 958 TYR 0.018 0.001 TYR B 596 ARG 0.006 0.000 ARG A 816 *********************** 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 276 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: B 304 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6040 (tp30) REVERT: B 435 MET cc_start: 0.7888 (mmm) cc_final: 0.7588 (mmp) REVERT: B 536 ARG cc_start: 0.6532 (mtm180) cc_final: 0.6285 (ptt180) REVERT: B 555 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6650 (t80) REVERT: B 652 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7372 (mtpt) REVERT: B 772 GLN cc_start: 0.7280 (mt0) cc_final: 0.7058 (mp10) REVERT: A 62 THR cc_start: 0.8497 (m) cc_final: 0.8288 (m) REVERT: A 76 MET cc_start: 0.8093 (ttm) cc_final: 0.7840 (ttp) REVERT: A 525 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6655 (ttp-170) REVERT: A 625 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7532 (ttp-170) REVERT: A 635 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: A 715 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7748 (ptp-170) REVERT: A 763 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7170 (mtm110) outliers start: 55 outliers final: 35 residues processed: 250 average time/residue: 1.4258 time to fit residues: 391.6778 Evaluate side-chains 252 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 138 LEU 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 452 VAL Chi-restraints excluded: chain B residue 538 LEU 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 574 SER Chi-restraints excluded: chain B residue 652 LYS 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 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 167 SER 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 512 PHE Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 626 MET 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 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 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 78 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 686 HIS ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15876 Z= 0.215 Angle : 0.526 7.986 21580 Z= 0.268 Chirality : 0.039 0.156 2514 Planarity : 0.004 0.046 2784 Dihedral : 4.475 51.660 2201 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.91 % Allowed : 19.01 % Favored : 78.09 % 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: 1.80 (0.19), residues: 2037 helix: 2.19 (0.15), residues: 1151 sheet: -0.35 (0.31), residues: 296 loop : 0.14 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.006 0.001 HIS B 955 PHE 0.014 0.001 PHE B 958 TYR 0.020 0.001 TYR B 596 ARG 0.005 0.000 ARG A 816 *********************** 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 268 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: B 404 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7770 (mt) REVERT: B 435 MET cc_start: 0.7871 (mmm) cc_final: 0.7583 (mmp) REVERT: B 478 MET cc_start: 0.8015 (mmp) cc_final: 0.7699 (mmp) REVERT: B 555 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6648 (t80) REVERT: B 652 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7367 (mtpt) REVERT: B 772 GLN cc_start: 0.7273 (mt0) cc_final: 0.7060 (mp10) REVERT: A 62 THR cc_start: 0.8555 (m) cc_final: 0.8344 (m) REVERT: A 525 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6650 (ttp-170) REVERT: A 625 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7528 (ttp-170) REVERT: A 635 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: A 715 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7743 (ptp-170) REVERT: A 763 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7244 (mtm110) REVERT: A 891 GLU cc_start: 0.7731 (tp30) cc_final: 0.7223 (mm-30) outliers start: 48 outliers final: 31 residues processed: 244 average time/residue: 1.4131 time to fit residues: 380.7846 Evaluate side-chains 249 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 222 THR Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 404 LEU 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 573 THR 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 692 ASP 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 167 SER 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 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 663 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 0.0060 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 164 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 686 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3308 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= 0.175 Angle : 0.515 7.675 21580 Z= 0.262 Chirality : 0.038 0.152 2514 Planarity : 0.004 0.044 2784 Dihedral : 4.432 51.146 2201 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.54 % Allowed : 19.61 % Favored : 77.85 % 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: 1.87 (0.19), residues: 2037 helix: 2.24 (0.15), residues: 1150 sheet: -0.20 (0.31), residues: 292 loop : 0.11 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 540 HIS 0.006 0.001 HIS B 955 PHE 0.012 0.001 PHE B 958 TYR 0.020 0.001 TYR A 356 ARG 0.005 0.000 ARG B 539 *********************** 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 272 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.706 Fit side-chains REVERT: B 435 MET cc_start: 0.7773 (mmm) cc_final: 0.7499 (mmp) REVERT: B 478 MET cc_start: 0.8023 (mmp) cc_final: 0.7695 (mmp) REVERT: B 652 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7363 (mtpt) REVERT: A 62 THR cc_start: 0.8503 (m) cc_final: 0.8264 (m) REVERT: A 80 SER cc_start: 0.8775 (p) cc_final: 0.8573 (m) REVERT: A 525 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6628 (ttp-170) REVERT: A 601 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: A 625 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7526 (ttp-170) REVERT: A 635 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: A 715 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7714 (ptp-170) REVERT: A 763 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7236 (mtm110) REVERT: A 891 GLU cc_start: 0.7729 (tp30) cc_final: 0.7212 (mm-30) outliers start: 42 outliers final: 25 residues processed: 256 average time/residue: 1.3924 time to fit residues: 392.0287 Evaluate side-chains 246 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR 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 692 ASP 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 167 SER Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 635 GLU 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 851 ASN Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 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 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 600 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3340 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= 0.210 Angle : 0.530 7.782 21580 Z= 0.270 Chirality : 0.039 0.155 2514 Planarity : 0.004 0.044 2784 Dihedral : 4.301 51.468 2199 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.24 % Allowed : 20.04 % Favored : 77.72 % 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: 1.83 (0.19), residues: 2037 helix: 2.19 (0.15), residues: 1150 sheet: -0.04 (0.33), residues: 269 loop : 0.00 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 540 HIS 0.006 0.001 HIS B 955 PHE 0.013 0.001 PHE B 958 TYR 0.022 0.001 TYR B 596 ARG 0.005 0.000 ARG B 539 ********************** 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 259 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 1.805 Fit side-chains REVERT: B 152 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.5844 (mt0) REVERT: B 435 MET cc_start: 0.7794 (mmm) cc_final: 0.7556 (mmp) REVERT: B 478 MET cc_start: 0.8025 (mmp) cc_final: 0.7700 (mmp) REVERT: B 555 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6748 (t80) REVERT: B 652 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7355 (mtpt) REVERT: A 62 THR cc_start: 0.8561 (m) cc_final: 0.8340 (m) REVERT: A 525 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6636 (ttp-170) REVERT: A 601 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7376 (mm-30) REVERT: A 625 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7603 (ttp-170) REVERT: A 635 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: A 763 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7256 (mtm110) REVERT: A 891 GLU cc_start: 0.7783 (tp30) cc_final: 0.7227 (mm-30) outliers start: 37 outliers final: 25 residues processed: 245 average time/residue: 1.3748 time to fit residues: 371.6417 Evaluate side-chains 243 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 83 SER 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 452 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR 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 844 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 635 GLU 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 851 ASN Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103529 restraints weight = 18429.781| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.49 r_work: 0.3003 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15876 Z= 0.268 Angle : 0.558 8.042 21580 Z= 0.285 Chirality : 0.040 0.162 2514 Planarity : 0.004 0.043 2784 Dihedral : 4.417 52.440 2199 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.42 % Allowed : 19.79 % Favored : 77.78 % 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: 1.69 (0.19), residues: 2037 helix: 2.10 (0.15), residues: 1150 sheet: -0.24 (0.32), residues: 268 loop : -0.04 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.006 0.001 HIS B 955 PHE 0.014 0.001 PHE B 958 TYR 0.023 0.002 TYR B 596 ARG 0.005 0.000 ARG A 816 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6788.91 seconds wall clock time: 121 minutes 57.51 seconds (7317.51 seconds total)