Starting phenix.real_space_refine on Fri Feb 16 14:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/02_2024/8f4n_28855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/02_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_28855/02_2024/8f4n_28855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/02_2024/8f4n_28855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/02_2024/8f4n_28855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4n_28855/02_2024/8f4n_28855.pdb" } 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 Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.35, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 6.08 Conformation dependent library (CDL) restraints added in 2.8 seconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 61.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 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: 6.57 Time building geometry restraints manager: 6.53 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: 99.84 - 106.67: 451 106.67 - 113.49: 8795 113.49 - 120.32: 5486 120.32 - 127.15: 6704 127.15 - 133.97: 144 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 2.520 nonbonded pdb=" OE1 GLU B 66 " pdb=" NH1 ARG B 816 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASN B 415 " pdb=" NH1 ARG B 418 " model vdw 2.284 2.520 nonbonded pdb=" OG1 THR A 46 " pdb=" OG1 THR A 128 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.294 2.440 ... (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 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: 2.090 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: 0.010 Extract box with map and model: 10.210 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 43.420 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.230 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 35 poor density : 463 time to evaluate : 1.736 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: 1.2569 time to fit residues: 674.5962 Evaluate side-chains 253 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 245 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN B 585 GLN B 700 GLN B 724 GLN B 735 GLN B 870 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN A 109 ASN A 112 GLN A 120 GLN A 124 ASN A 254 ASN A 360 GLN A 439 GLN A 516 ASN A 517 GLN ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15876 Z= 0.271 Angle : 0.551 8.151 21580 Z= 0.286 Chirality : 0.040 0.157 2514 Planarity : 0.004 0.032 2784 Dihedral : 4.467 58.206 2203 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.66 % Allowed : 13.86 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.19), residues: 2037 helix: 2.38 (0.15), residues: 1150 sheet: -0.18 (0.30), residues: 298 loop : 0.34 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.006 0.001 HIS A 955 PHE 0.018 0.001 PHE A 4 TYR 0.017 0.002 TYR A 182 ARG 0.005 0.001 ARG A 636 *********************** 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 338 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 261 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: B 81 GLN cc_start: 0.7127 (mp10) cc_final: 0.6820 (mp10) REVERT: B 145 THR cc_start: 0.7215 (OUTLIER) cc_final: 0.6975 (p) REVERT: B 152 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.5995 (mt0) REVERT: B 192 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6548 (mmtp) REVERT: B 456 MET cc_start: 0.8297 (mtm) cc_final: 0.7791 (mtm) REVERT: B 478 MET cc_start: 0.8004 (mmp) cc_final: 0.7542 (mmp) REVERT: B 516 ASN cc_start: 0.8046 (m-40) cc_final: 0.7827 (m110) REVERT: B 555 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6511 (t80) REVERT: B 568 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8037 (mtm-85) REVERT: B 652 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7452 (mtpt) REVERT: B 839 MET cc_start: 0.8780 (mtp) cc_final: 0.8519 (mtm) REVERT: B 920 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: A 435 MET cc_start: 0.8117 (mmm) cc_final: 0.7793 (mmm) REVERT: A 478 MET cc_start: 0.8216 (mmm) cc_final: 0.7865 (mmp) REVERT: A 635 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6738 (mt-10) REVERT: A 659 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6971 (mt-10) outliers start: 77 outliers final: 29 residues processed: 314 average time/residue: 1.3826 time to fit residues: 476.7795 Evaluate side-chains 265 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 227 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 60 THR 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 131 LYS 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 192 LYS 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 568 ARG Chi-restraints excluded: chain B residue 582 THR 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 265 VAL Chi-restraints excluded: chain A residue 343 THR 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 663 ILE Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 742 ASP 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: 4.9990 chunk 57 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 30.0000 chunk 184 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 735 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 120 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 584 GLN A 745 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15876 Z= 0.365 Angle : 0.582 8.432 21580 Z= 0.300 Chirality : 0.042 0.167 2514 Planarity : 0.004 0.040 2784 Dihedral : 4.692 57.224 2201 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.27 % Allowed : 14.77 % Favored : 79.96 % 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: 1.61 (0.19), residues: 2037 helix: 2.03 (0.14), residues: 1153 sheet: -0.54 (0.30), residues: 300 loop : 0.14 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 540 HIS 0.004 0.001 HIS B 319 PHE 0.019 0.002 PHE A 4 TYR 0.017 0.002 TYR B 596 ARG 0.005 0.001 ARG A 636 *********************** 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 323 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 236 time to evaluate : 1.999 Fit side-chains REVERT: B 81 GLN cc_start: 0.7112 (mp10) cc_final: 0.6806 (mp10) REVERT: B 152 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.5921 (mt0) REVERT: B 192 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6453 (mmtp) REVERT: B 280 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7128 (mtp-110) REVERT: B 456 MET cc_start: 0.8390 (mtm) cc_final: 0.7963 (mtm) REVERT: B 555 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6573 (t80) REVERT: B 568 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8020 (mtm-85) REVERT: B 652 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7644 (mtpt) REVERT: B 839 MET cc_start: 0.8786 (mtp) cc_final: 0.8544 (mtm) REVERT: A 435 MET cc_start: 0.8174 (mmm) cc_final: 0.7851 (mmm) REVERT: A 525 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6527 (ttp80) REVERT: A 635 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6652 (mt-10) REVERT: A 659 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6970 (mt-10) outliers start: 87 outliers final: 41 residues processed: 289 average time/residue: 1.4921 time to fit residues: 472.0473 Evaluate side-chains 269 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 60 THR 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 131 LYS 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 192 LYS 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 280 ARG 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 568 ARG Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL 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 116 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 495 THR 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 646 ILE Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 663 ILE 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 809 THR Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 67 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN A 360 GLN ** A 437 GLN ** 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: 0.7773 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15876 Z= 0.232 Angle : 0.521 8.267 21580 Z= 0.266 Chirality : 0.039 0.153 2514 Planarity : 0.004 0.039 2784 Dihedral : 4.571 55.182 2201 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.18 % Allowed : 16.34 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.19), residues: 2037 helix: 2.17 (0.15), residues: 1152 sheet: -0.34 (0.31), residues: 287 loop : 0.14 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 540 HIS 0.003 0.001 HIS B 319 PHE 0.016 0.001 PHE A 4 TYR 0.017 0.001 TYR B 596 ARG 0.011 0.000 ARG B 8 *********************** 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 301 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 232 time to evaluate : 1.740 Fit side-chains REVERT: B 152 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.5982 (mt0) REVERT: B 192 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6311 (mmtp) REVERT: B 456 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: B 478 MET cc_start: 0.8087 (mmp) cc_final: 0.7607 (mmp) REVERT: B 555 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6571 (t80) REVERT: B 568 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8037 (mtm-85) REVERT: B 652 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7506 (mtpt) REVERT: B 839 MET cc_start: 0.8764 (mtp) cc_final: 0.8563 (mtm) REVERT: A 261 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6463 (mtt90) REVERT: A 435 MET cc_start: 0.8139 (mmm) cc_final: 0.7777 (mmm) REVERT: A 525 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6524 (ttp80) REVERT: A 635 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6687 (mt-10) outliers start: 69 outliers final: 31 residues processed: 272 average time/residue: 1.4133 time to fit residues: 421.1645 Evaluate side-chains 248 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 149 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 192 LYS 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 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 766 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 143 VAL Chi-restraints excluded: chain A residue 150 ASP 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 528 LYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 676 SER 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 920 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 167 optimal weight: 0.1980 chunk 135 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 67 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 735 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15876 Z= 0.193 Angle : 0.503 8.065 21580 Z= 0.255 Chirality : 0.038 0.152 2514 Planarity : 0.004 0.039 2784 Dihedral : 4.496 54.029 2201 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.81 % Allowed : 17.13 % Favored : 79.06 % 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: 1.85 (0.19), residues: 2037 helix: 2.24 (0.15), residues: 1152 sheet: -0.30 (0.31), residues: 289 loop : 0.10 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 540 HIS 0.002 0.001 HIS B 955 PHE 0.022 0.001 PHE B 958 TYR 0.019 0.001 TYR B 596 ARG 0.008 0.000 ARG B 813 *********************** 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 293 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 230 time to evaluate : 1.583 Fit side-chains REVERT: B 152 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.5818 (mt0) REVERT: B 280 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7125 (mtp-110) REVERT: B 304 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6039 (tp30) REVERT: B 456 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7936 (mtm) REVERT: B 478 MET cc_start: 0.8088 (mmp) cc_final: 0.7846 (mmp) REVERT: B 536 ARG cc_start: 0.6704 (mtm180) cc_final: 0.6410 (ptt180) REVERT: B 555 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6595 (t80) REVERT: B 652 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7418 (mtpt) REVERT: B 839 MET cc_start: 0.8751 (mtp) cc_final: 0.8541 (mtm) REVERT: A 69 MET cc_start: 0.8155 (mmt) cc_final: 0.7613 (mmt) REVERT: A 261 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6416 (mtt90) REVERT: A 435 MET cc_start: 0.8141 (mmm) cc_final: 0.7888 (mmm) REVERT: A 525 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6494 (ttp80) REVERT: A 635 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: A 715 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7718 (ptp-170) outliers start: 63 outliers final: 32 residues processed: 265 average time/residue: 1.4144 time to fit residues: 412.4687 Evaluate side-chains 255 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR 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 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 280 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 772 GLN 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 150 ASP Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 198 MET 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 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 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 920 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN B 926 GLN A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15876 Z= 0.216 Angle : 0.510 7.717 21580 Z= 0.258 Chirality : 0.039 0.154 2514 Planarity : 0.004 0.039 2784 Dihedral : 4.484 53.106 2201 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.36 % Allowed : 17.25 % Favored : 78.39 % 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: 2.23 (0.15), residues: 1152 sheet: -0.31 (0.30), residues: 291 loop : 0.08 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.005 0.001 HIS B 955 PHE 0.016 0.001 PHE B 958 TYR 0.019 0.001 TYR B 596 ARG 0.005 0.000 ARG A 816 *********************** 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 299 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 227 time to evaluate : 1.622 Fit side-chains REVERT: B 280 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7100 (mtp-110) REVERT: B 304 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6072 (tp30) REVERT: B 456 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7950 (mtm) REVERT: B 536 ARG cc_start: 0.6588 (mtm180) cc_final: 0.6369 (ptt180) REVERT: B 555 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6617 (t80) REVERT: B 652 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7408 (mtpt) REVERT: A 69 MET cc_start: 0.8036 (mmt) cc_final: 0.7451 (mmt) REVERT: A 261 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6397 (mtt90) REVERT: A 435 MET cc_start: 0.8135 (mmm) cc_final: 0.7774 (mmm) REVERT: A 525 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6446 (ttp80) REVERT: A 601 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: A 625 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7547 (ttp-170) REVERT: A 635 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6636 (mt-10) REVERT: A 715 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7758 (ptp-170) outliers start: 72 outliers final: 40 residues processed: 263 average time/residue: 1.3883 time to fit residues: 401.0144 Evaluate side-chains 263 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 MET 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 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 198 MET 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 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 601 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 731 GLN B 735 GLN B 967 GLN A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15876 Z= 0.199 Angle : 0.505 7.514 21580 Z= 0.255 Chirality : 0.038 0.152 2514 Planarity : 0.003 0.039 2784 Dihedral : 4.441 52.957 2201 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.06 % Allowed : 18.46 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.26 (0.15), residues: 1151 sheet: -0.33 (0.30), residues: 297 loop : 0.10 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.004 0.001 HIS B 955 PHE 0.016 0.001 PHE B 958 TYR 0.025 0.001 TYR A 356 ARG 0.007 0.000 ARG B 813 *********************** 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 291 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 1.879 Fit side-chains REVERT: B 280 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7134 (mtp-110) REVERT: B 304 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6071 (tp30) REVERT: B 456 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7937 (mtm) REVERT: B 478 MET cc_start: 0.7982 (mmp) cc_final: 0.7625 (mmp) REVERT: B 536 ARG cc_start: 0.6473 (mtm180) cc_final: 0.6222 (ptt180) REVERT: B 555 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6651 (t80) REVERT: B 652 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7370 (mtpt) REVERT: A 69 MET cc_start: 0.8007 (mmt) cc_final: 0.7430 (mmt) REVERT: A 261 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6360 (mtt90) REVERT: A 363 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7684 (mtt90) REVERT: A 435 MET cc_start: 0.8081 (mmm) cc_final: 0.7824 (mmm) REVERT: A 525 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6445 (ttp80) REVERT: A 625 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7543 (ttp-170) REVERT: A 635 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: A 715 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7702 (ptp-170) REVERT: A 891 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7127 (mm-30) outliers start: 67 outliers final: 32 residues processed: 257 average time/residue: 1.4168 time to fit residues: 400.7919 Evaluate side-chains 256 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 213 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 THR 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 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 133 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN A 59 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 0.044 15876 Z= 0.207 Angle : 0.511 7.524 21580 Z= 0.259 Chirality : 0.039 0.159 2514 Planarity : 0.003 0.039 2784 Dihedral : 4.453 53.093 2201 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.93 % Allowed : 18.58 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.15), residues: 1151 sheet: -0.25 (0.31), residues: 287 loop : 0.08 (0.26), residues: 599 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 0.021 0.001 TYR B 596 ARG 0.005 0.000 ARG B 813 *********************** 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 285 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 220 time to evaluate : 1.996 Fit side-chains REVERT: B 280 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7169 (mtp-110) REVERT: B 304 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6142 (tp30) REVERT: B 404 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 435 MET cc_start: 0.7860 (mmm) cc_final: 0.7619 (mmp) REVERT: B 456 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7915 (mtm) REVERT: B 478 MET cc_start: 0.8069 (mmp) cc_final: 0.7722 (mmp) REVERT: B 555 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6654 (t80) REVERT: B 652 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7371 (mtpt) REVERT: A 69 MET cc_start: 0.7985 (mmt) cc_final: 0.7442 (mmt) REVERT: A 261 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6349 (mtt90) REVERT: A 363 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7676 (mtt90) REVERT: A 435 MET cc_start: 0.8114 (mmm) cc_final: 0.7781 (mmm) REVERT: A 439 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7371 (tp-100) REVERT: A 525 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6443 (ttp80) REVERT: A 625 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7589 (ttp-170) REVERT: A 635 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6644 (mt-10) REVERT: A 715 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7712 (ptp-170) REVERT: A 891 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: A 959 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6914 (tt0) outliers start: 65 outliers final: 39 residues processed: 252 average time/residue: 1.4340 time to fit residues: 396.6135 Evaluate side-chains 266 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 213 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 THR 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 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 858 THR 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 116 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 439 GLN 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 626 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1013 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN B 686 HIS B 735 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15876 Z= 0.256 Angle : 0.531 7.747 21580 Z= 0.270 Chirality : 0.040 0.154 2514 Planarity : 0.004 0.040 2784 Dihedral : 4.514 53.602 2201 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.69 % Allowed : 18.83 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.19), residues: 2037 helix: 2.14 (0.15), residues: 1152 sheet: -0.31 (0.30), residues: 300 loop : 0.09 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 540 HIS 0.007 0.001 HIS B 955 PHE 0.014 0.001 PHE B 853 TYR 0.023 0.001 TYR B 596 ARG 0.006 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 280 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 219 time to evaluate : 1.778 Fit side-chains REVERT: B 152 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6031 (mt0) REVERT: B 280 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7235 (mtp-110) REVERT: B 304 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6148 (tp30) REVERT: B 435 MET cc_start: 0.7878 (mmm) cc_final: 0.7629 (mmp) REVERT: B 456 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7944 (mtm) REVERT: B 478 MET cc_start: 0.8121 (mmp) cc_final: 0.7867 (mmp) REVERT: B 555 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6609 (t80) REVERT: B 652 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7468 (mtpt) REVERT: A 69 MET cc_start: 0.7971 (mmt) cc_final: 0.7417 (mmt) REVERT: A 261 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6375 (mtt90) REVERT: A 363 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7664 (mtt90) REVERT: A 435 MET cc_start: 0.8059 (mmm) cc_final: 0.7708 (mmm) REVERT: A 525 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6449 (ttp80) REVERT: A 625 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7610 (ttp-170) REVERT: A 635 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: A 959 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6913 (tt0) outliers start: 61 outliers final: 39 residues processed: 249 average time/residue: 1.4013 time to fit residues: 382.9354 Evaluate side-chains 269 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 THR 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 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 ARG 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 456 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 858 THR 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 116 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 150 ASP 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 363 ARG Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 MET 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 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 797 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1013 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 0.0050 chunk 127 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B 686 HIS B 735 GLN B 967 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3315 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= 0.183 Angle : 0.508 9.125 21580 Z= 0.256 Chirality : 0.038 0.146 2514 Planarity : 0.003 0.039 2784 Dihedral : 4.437 53.567 2201 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.85 % Allowed : 19.67 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2037 helix: 2.24 (0.15), residues: 1150 sheet: -0.01 (0.32), residues: 270 loop : 0.02 (0.26), residues: 617 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 0.013 0.001 PHE B 853 TYR 0.022 0.001 TYR B 596 ARG 0.005 0.000 ARG B 813 ********************** 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 268 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 1.719 Fit side-chains REVERT: B 280 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7094 (mtp-110) REVERT: B 304 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6138 (tp30) REVERT: B 435 MET cc_start: 0.7733 (mmm) cc_final: 0.7473 (mmp) REVERT: B 456 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7856 (mtm) REVERT: B 478 MET cc_start: 0.8003 (mmp) cc_final: 0.7702 (mmp) REVERT: B 652 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7358 (mtpt) REVERT: A 69 MET cc_start: 0.7942 (mmt) cc_final: 0.7350 (mmt) REVERT: A 261 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6332 (mtt90) REVERT: A 435 MET cc_start: 0.8143 (mmm) cc_final: 0.7882 (mmm) REVERT: A 525 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6418 (ttp80) REVERT: A 625 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7592 (ttp-170) REVERT: A 635 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6602 (mt-10) REVERT: A 891 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: A 959 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6906 (tt0) outliers start: 47 outliers final: 27 residues processed: 245 average time/residue: 1.3970 time to fit residues: 376.4997 Evaluate side-chains 251 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 138 LEU 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 280 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 858 THR 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 143 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 164 ASP 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 528 LYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 959 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 148 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 735 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN A 123 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.105456 restraints weight = 18361.872| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.48 r_work: 0.3021 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3335 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= 0.198 Angle : 0.508 7.732 21580 Z= 0.256 Chirality : 0.039 0.151 2514 Planarity : 0.003 0.039 2784 Dihedral : 4.284 53.804 2199 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.66 % Allowed : 20.04 % Favored : 77.30 % 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: 2.22 (0.15), residues: 1150 sheet: 0.01 (0.32), residues: 270 loop : -0.01 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 540 HIS 0.006 0.001 HIS B 955 PHE 0.014 0.001 PHE B 853 TYR 0.022 0.001 TYR B 596 ARG 0.005 0.000 ARG B 813 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6666.53 seconds wall clock time: 118 minutes 43.60 seconds (7123.60 seconds total)