Starting phenix.real_space_refine on Tue Jul 29 05:36:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vsh_32111/07_2025/7vsh_32111.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vsh_32111/07_2025/7vsh_32111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2025/7vsh_32111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2025/7vsh_32111.map" model { file = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2025/7vsh_32111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2025/7vsh_32111.cif" } resolution = 3.4 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= 0.003 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 58 5.16 5 C 7106 2.51 5 N 1800 2.21 5 O 2022 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10992 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8300 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 1002} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 25, 'TRANS': 298} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 1, '17F': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'17F:plan-5': 1, '17F:plan-1': 1, '17F:plan-2': 1, '17F:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.15, per 1000 atoms: 0.65 Number of scatterers: 10992 At special positions: 0 Unit cell: (110.39, 87.15, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2022 8.00 N 1800 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " NAG B 2 " - " MAN B 3 " BETA1-3 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.6 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 49.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 88 through 122 Proline residue: A 94 - end of helix removed outlier: 3.605A pdb=" N VAL A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.683A pdb=" N ASN A 273 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 282 through 314 removed outlier: 3.565A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.020A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.613A pdb=" N GLY A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.527A pdb=" N LEU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.725A pdb=" N THR A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 removed outlier: 3.719A pdb=" N ILE A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 574 through 591 removed outlier: 3.714A pdb=" N ILE A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.531A pdb=" N ARG A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 633 removed outlier: 3.524A pdb=" N PHE A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.621A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 726 removed outlier: 3.696A pdb=" N LYS A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 718 " --> pdb=" O ARG A 714 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.733A pdb=" N ASN A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 839 through 844 Processing helix chain 'A' and resid 853 through 861 removed outlier: 4.346A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 895 removed outlier: 3.599A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 4.160A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 914 removed outlier: 4.803A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 924 removed outlier: 3.621A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.670A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 removed outlier: 3.887A pdb=" N SER A 946 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 removed outlier: 3.665A pdb=" N LEU A 951 " --> pdb=" O ASN A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 948 through 951' Processing helix chain 'A' and resid 952 through 976 removed outlier: 3.596A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 980 removed outlier: 3.618A pdb=" N THR A 980 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 980' Processing helix chain 'A' and resid 991 through 1015 removed outlier: 3.595A pdb=" N PHE A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.635A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 3.820A pdb=" N TRP A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1090 removed outlier: 3.543A pdb=" N ILE A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 75 Proline residue: C 52 - end of helix removed outlier: 4.319A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.858A pdb=" N ILE C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 removed outlier: 4.024A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.516A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.566A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.804A pdb=" N CYS C 157 " --> pdb=" O SER C 154 " (cutoff:3.500A) Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.550A pdb=" N LYS C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.785A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.685A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.706A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.613A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 322 through 350 removed outlier: 4.747A pdb=" N GLY C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.515A pdb=" N LEU A 239 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 11.755A pdb=" N THR A 124 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN A 150 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS A 256 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER A 164 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 260 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP A 158 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.620A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.657A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 670 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N CYS A 787 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 672 " --> pdb=" O CYS A 787 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 422 removed outlier: 5.594A pdb=" N SER A 418 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A 651 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 647 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 512 removed outlier: 5.641A pdb=" N LEU A 534 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 552 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 540 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A 546 " --> pdb=" O PHE A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 removed outlier: 7.150A pdb=" N VAL A 598 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.558A pdb=" N ARG C 307 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 104 through 109 removed outlier: 4.520A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 3.76 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: 3451 1.34 - 1.46: 2146 1.46 - 1.58: 5555 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11243 Sorted by residual: bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.801 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.797 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C3 NAG B 1 " pdb=" O3 NAG B 1 " ideal model delta sigma weight residual 1.403 1.443 -0.040 2.00e-02 2.50e+03 3.90e+00 ... (remaining 11238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.19: 15226 14.19 - 28.38: 4 28.38 - 42.57: 0 42.57 - 56.76: 0 56.76 - 70.94: 2 Bond angle restraints: 15232 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.62 -70.94 3.00e+00 1.11e-01 5.59e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.50 -69.87 3.00e+00 1.11e-01 5.42e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.06 20.15 3.00e+00 1.11e-01 4.51e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.58 20.01 3.00e+00 1.11e-01 4.45e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 89.68 19.34 3.00e+00 1.11e-01 4.15e+01 ... (remaining 15227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.22: 6342 23.22 - 46.44: 348 46.44 - 69.66: 39 69.66 - 92.88: 17 92.88 - 116.10: 11 Dihedral angle restraints: 6757 sinusoidal: 2788 harmonic: 3969 Sorted by residual: dihedral pdb=" O2 MAN B 3 " pdb=" C2 MAN B 3 " pdb=" C3 MAN B 3 " pdb=" O3 MAN B 3 " ideal model delta sinusoidal sigma weight residual -57.63 58.47 -116.10 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C4 MAN B 3 " pdb=" C2 MAN B 3 " pdb=" C3 MAN B 3 " pdb=" O2 MAN B 3 " ideal model delta sinusoidal sigma weight residual -64.75 -179.48 114.73 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C1 MAN B 3 " pdb=" C2 MAN B 3 " pdb=" C3 MAN B 3 " pdb=" O3 MAN B 3 " ideal model delta sinusoidal sigma weight residual -176.02 -62.95 -113.07 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 6754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1561 0.072 - 0.145: 155 0.145 - 0.217: 5 0.217 - 0.289: 1 0.289 - 0.362: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O3 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.27e+02 chirality pdb=" C1 MAN B 3 " pdb=" O3 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.50e+01 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1720 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.320 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG C 401 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.317 2.00e-02 2.50e+03 2.66e-01 8.84e+02 pdb=" C7 NAG C 402 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.194 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.456 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.218 2.00e-02 2.50e+03 1.85e-01 4.30e+02 pdb=" C7 NAG B 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.303 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.169 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 52 2.55 - 3.14: 8655 3.14 - 3.73: 16581 3.73 - 4.31: 24092 4.31 - 4.90: 39963 Nonbonded interactions: 89343 Sorted by model distance: nonbonded pdb="MG MG A1100 " pdb=" F1 ALF A1101 " model vdw 1.964 2.120 nonbonded pdb=" OH TYR A 311 " pdb=" OD2 ASP A 343 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN C 176 " pdb=" OD1 ASN C 235 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR A 484 " pdb=" O ALA A 487 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A 879 " pdb=" OE1 GLU A 966 " model vdw 2.281 3.040 ... (remaining 89338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.110 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.005 0.117 11251 Z= 0.212 Angle : 1.088 70.944 15253 Z= 0.454 Chirality : 0.044 0.362 1723 Planarity : 0.011 0.274 1917 Dihedral : 15.177 116.102 4186 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.25 % Allowed : 0.08 % Favored : 99.67 % 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: -1.53 (0.22), residues: 1342 helix: -0.57 (0.21), residues: 565 sheet: -0.13 (0.37), residues: 192 loop : -1.70 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 470 PHE 0.029 0.002 PHE A 978 TYR 0.016 0.002 TYR A1054 ARG 0.004 0.001 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 3) link_NAG-ASN : angle 3.30729 ( 9) link_ALPHA1-3 : bond 0.01926 ( 1) link_ALPHA1-3 : angle 2.98823 ( 3) hydrogen bonds : bond 0.26629 ( 476) hydrogen bonds : angle 8.57156 ( 1353) SS BOND : bond 0.00614 ( 3) SS BOND : angle 0.87965 ( 6) link_BETA1-3 : bond 0.04376 ( 1) link_BETA1-3 : angle 10.37699 ( 3) covalent geometry : bond 0.00458 (11243) covalent geometry : angle 1.07467 (15232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.523 Fit side-chains REVERT: A 205 LEU cc_start: 0.7316 (tp) cc_final: 0.7008 (tp) REVERT: A 629 MET cc_start: 0.6772 (mmp) cc_final: 0.5886 (mtp) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.3356 time to fit residues: 71.2976 Evaluate side-chains 113 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 0.0030 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 457 ASN A 536 HIS A 584 HIS ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117659 restraints weight = 14371.838| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.32 r_work: 0.3078 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11251 Z= 0.231 Angle : 0.672 8.541 15253 Z= 0.347 Chirality : 0.047 0.314 1723 Planarity : 0.005 0.044 1917 Dihedral : 9.534 78.059 1581 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.17 % Allowed : 6.91 % Favored : 91.92 % 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: -0.98 (0.22), residues: 1342 helix: 0.18 (0.21), residues: 588 sheet: -0.04 (0.36), residues: 195 loop : -1.76 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 323 HIS 0.014 0.002 HIS A 536 PHE 0.024 0.002 PHE A 978 TYR 0.015 0.002 TYR A 324 ARG 0.004 0.001 ARG A 572 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 3) link_NAG-ASN : angle 4.40508 ( 9) link_ALPHA1-3 : bond 0.00206 ( 1) link_ALPHA1-3 : angle 2.61115 ( 3) hydrogen bonds : bond 0.05942 ( 476) hydrogen bonds : angle 5.50430 ( 1353) SS BOND : bond 0.00647 ( 3) SS BOND : angle 1.35022 ( 6) link_BETA1-3 : bond 0.00213 ( 1) link_BETA1-3 : angle 3.01456 ( 3) covalent geometry : bond 0.00544 (11243) covalent geometry : angle 0.66089 (15232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.203 Fit side-chains REVERT: A 628 LYS cc_start: 0.7254 (ttpp) cc_final: 0.6830 (ttpp) REVERT: A 716 HIS cc_start: 0.6437 (m90) cc_final: 0.6207 (m90) REVERT: A 942 TYR cc_start: 0.7726 (m-80) cc_final: 0.7436 (m-80) REVERT: C 55 PHE cc_start: 0.7242 (m-80) cc_final: 0.6857 (m-80) outliers start: 14 outliers final: 12 residues processed: 129 average time/residue: 0.2432 time to fit residues: 44.7978 Evaluate side-chains 116 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120160 restraints weight = 14364.505| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.14 r_work: 0.3142 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11251 Z= 0.127 Angle : 0.567 7.186 15253 Z= 0.288 Chirality : 0.042 0.200 1723 Planarity : 0.004 0.035 1917 Dihedral : 7.325 74.680 1581 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.08 % Allowed : 9.99 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1342 helix: 0.86 (0.21), residues: 575 sheet: 0.06 (0.36), residues: 196 loop : -1.78 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS A 536 PHE 0.020 0.001 PHE A 421 TYR 0.017 0.001 TYR A 324 ARG 0.003 0.000 ARG A 572 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 3) link_NAG-ASN : angle 3.53533 ( 9) link_ALPHA1-3 : bond 0.00812 ( 1) link_ALPHA1-3 : angle 2.20807 ( 3) hydrogen bonds : bond 0.04699 ( 476) hydrogen bonds : angle 4.92814 ( 1353) SS BOND : bond 0.00464 ( 3) SS BOND : angle 0.89933 ( 6) link_BETA1-3 : bond 0.00386 ( 1) link_BETA1-3 : angle 2.84101 ( 3) covalent geometry : bond 0.00281 (11243) covalent geometry : angle 0.55806 (15232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.239 Fit side-chains REVERT: A 258 TYR cc_start: 0.8178 (m-10) cc_final: 0.7924 (m-10) REVERT: A 678 MET cc_start: 0.8337 (tmm) cc_final: 0.8026 (tmm) REVERT: A 716 HIS cc_start: 0.6518 (m90) cc_final: 0.6295 (m90) REVERT: A 942 TYR cc_start: 0.7844 (m-80) cc_final: 0.7592 (m-80) REVERT: C 55 PHE cc_start: 0.7151 (m-80) cc_final: 0.6909 (m-80) REVERT: C 60 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8099 (mt) REVERT: C 303 TYR cc_start: 0.8630 (m-80) cc_final: 0.8167 (m-80) outliers start: 13 outliers final: 9 residues processed: 132 average time/residue: 0.2367 time to fit residues: 45.5265 Evaluate side-chains 121 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.0870 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119086 restraints weight = 14264.551| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.19 r_work: 0.3128 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11251 Z= 0.152 Angle : 0.564 7.447 15253 Z= 0.290 Chirality : 0.043 0.180 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.941 73.630 1581 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.25 % Allowed : 11.82 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1342 helix: 0.93 (0.21), residues: 582 sheet: 0.08 (0.36), residues: 193 loop : -1.69 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.004 0.001 HIS A 828 PHE 0.016 0.001 PHE A 633 TYR 0.015 0.001 TYR A 722 ARG 0.009 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 3) link_NAG-ASN : angle 3.47209 ( 9) link_ALPHA1-3 : bond 0.00695 ( 1) link_ALPHA1-3 : angle 2.01875 ( 3) hydrogen bonds : bond 0.04478 ( 476) hydrogen bonds : angle 4.72993 ( 1353) SS BOND : bond 0.00444 ( 3) SS BOND : angle 1.01453 ( 6) link_BETA1-3 : bond 0.00274 ( 1) link_BETA1-3 : angle 3.05070 ( 3) covalent geometry : bond 0.00356 (11243) covalent geometry : angle 0.55510 (15232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.270 Fit side-chains REVERT: A 258 TYR cc_start: 0.8168 (m-10) cc_final: 0.7832 (m-10) REVERT: A 629 MET cc_start: 0.6551 (mmt) cc_final: 0.6081 (mmm) REVERT: A 678 MET cc_start: 0.8330 (tmm) cc_final: 0.7990 (tmm) REVERT: A 942 TYR cc_start: 0.7857 (m-80) cc_final: 0.7559 (m-80) REVERT: C 55 PHE cc_start: 0.7106 (m-80) cc_final: 0.6896 (m-80) outliers start: 15 outliers final: 11 residues processed: 135 average time/residue: 0.2328 time to fit residues: 45.9249 Evaluate side-chains 122 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 108 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119769 restraints weight = 14179.867| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.09 r_work: 0.3154 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11251 Z= 0.113 Angle : 0.525 7.003 15253 Z= 0.270 Chirality : 0.042 0.184 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.729 72.685 1581 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.25 % Allowed : 12.74 % Favored : 86.01 % 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: -0.23 (0.23), residues: 1342 helix: 1.12 (0.21), residues: 582 sheet: 0.18 (0.36), residues: 196 loop : -1.66 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.012 0.001 HIS A 716 PHE 0.015 0.001 PHE A 633 TYR 0.016 0.001 TYR A 324 ARG 0.009 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 3) link_NAG-ASN : angle 3.50284 ( 9) link_ALPHA1-3 : bond 0.00772 ( 1) link_ALPHA1-3 : angle 1.79058 ( 3) hydrogen bonds : bond 0.03958 ( 476) hydrogen bonds : angle 4.54560 ( 1353) SS BOND : bond 0.00380 ( 3) SS BOND : angle 0.87069 ( 6) link_BETA1-3 : bond 0.00381 ( 1) link_BETA1-3 : angle 2.89816 ( 3) covalent geometry : bond 0.00253 (11243) covalent geometry : angle 0.51565 (15232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.286 Fit side-chains REVERT: A 252 LYS cc_start: 0.8054 (tppt) cc_final: 0.7092 (tmtt) REVERT: A 258 TYR cc_start: 0.8195 (m-10) cc_final: 0.7940 (m-10) REVERT: A 629 MET cc_start: 0.6670 (mmt) cc_final: 0.6419 (mmt) REVERT: A 631 LYS cc_start: 0.7416 (ttpt) cc_final: 0.6680 (mtmt) REVERT: A 678 MET cc_start: 0.8327 (tmm) cc_final: 0.8000 (tmm) REVERT: A 942 TYR cc_start: 0.7834 (m-80) cc_final: 0.7551 (m-80) REVERT: A 943 MET cc_start: 0.8143 (tpt) cc_final: 0.6048 (tpt) outliers start: 15 outliers final: 11 residues processed: 131 average time/residue: 0.2475 time to fit residues: 47.0047 Evaluate side-chains 124 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 30 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118833 restraints weight = 14314.124| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.36 r_work: 0.3110 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11251 Z= 0.161 Angle : 0.557 7.355 15253 Z= 0.285 Chirality : 0.043 0.187 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.762 72.635 1581 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.67 % Allowed : 13.57 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.25 (0.23), residues: 1342 helix: 1.10 (0.21), residues: 577 sheet: 0.24 (0.37), residues: 193 loop : -1.67 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.010 0.001 HIS A 716 PHE 0.019 0.002 PHE A 421 TYR 0.014 0.001 TYR A 324 ARG 0.004 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 3) link_NAG-ASN : angle 3.53447 ( 9) link_ALPHA1-3 : bond 0.00733 ( 1) link_ALPHA1-3 : angle 2.09586 ( 3) hydrogen bonds : bond 0.04286 ( 476) hydrogen bonds : angle 4.56846 ( 1353) SS BOND : bond 0.00444 ( 3) SS BOND : angle 1.03543 ( 6) link_BETA1-3 : bond 0.00084 ( 1) link_BETA1-3 : angle 3.07922 ( 3) covalent geometry : bond 0.00383 (11243) covalent geometry : angle 0.54795 (15232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.217 Fit side-chains REVERT: A 252 LYS cc_start: 0.8109 (tppt) cc_final: 0.7126 (tmtt) REVERT: A 258 TYR cc_start: 0.8217 (m-10) cc_final: 0.7935 (m-10) REVERT: A 629 MET cc_start: 0.6878 (mmt) cc_final: 0.6629 (mmt) REVERT: A 631 LYS cc_start: 0.7407 (ttpt) cc_final: 0.6659 (mtmt) REVERT: A 678 MET cc_start: 0.8314 (tmm) cc_final: 0.7958 (tmm) REVERT: A 942 TYR cc_start: 0.7919 (m-80) cc_final: 0.7545 (m-80) outliers start: 20 outliers final: 17 residues processed: 136 average time/residue: 0.2294 time to fit residues: 45.3282 Evaluate side-chains 129 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 53 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120796 restraints weight = 14426.299| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.24 r_work: 0.3133 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11251 Z= 0.132 Angle : 0.535 6.925 15253 Z= 0.274 Chirality : 0.043 0.181 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.656 72.186 1581 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.58 % Allowed : 13.91 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1342 helix: 1.25 (0.22), residues: 571 sheet: 0.25 (0.37), residues: 194 loop : -1.66 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.010 0.001 HIS A 716 PHE 0.016 0.001 PHE A 633 TYR 0.015 0.001 TYR A 324 ARG 0.009 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 3) link_NAG-ASN : angle 3.57970 ( 9) link_ALPHA1-3 : bond 0.00570 ( 1) link_ALPHA1-3 : angle 1.93447 ( 3) hydrogen bonds : bond 0.03996 ( 476) hydrogen bonds : angle 4.47295 ( 1353) SS BOND : bond 0.00423 ( 3) SS BOND : angle 0.94963 ( 6) link_BETA1-3 : bond 0.00246 ( 1) link_BETA1-3 : angle 3.01284 ( 3) covalent geometry : bond 0.00308 (11243) covalent geometry : angle 0.52583 (15232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.423 Fit side-chains REVERT: A 145 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8269 (p0) REVERT: A 250 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7955 (t) REVERT: A 252 LYS cc_start: 0.8059 (tppt) cc_final: 0.7122 (tmtt) REVERT: A 258 TYR cc_start: 0.8204 (m-10) cc_final: 0.7866 (m-10) REVERT: A 629 MET cc_start: 0.6789 (mmt) cc_final: 0.6531 (mmt) REVERT: A 631 LYS cc_start: 0.7407 (ttpt) cc_final: 0.6615 (mtmt) REVERT: A 678 MET cc_start: 0.8309 (tmm) cc_final: 0.7961 (tmm) REVERT: A 942 TYR cc_start: 0.7897 (m-80) cc_final: 0.7533 (m-80) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.2366 time to fit residues: 44.9421 Evaluate side-chains 124 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120465 restraints weight = 14195.226| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.25 r_work: 0.3151 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11251 Z= 0.116 Angle : 0.525 6.957 15253 Z= 0.269 Chirality : 0.042 0.185 1723 Planarity : 0.004 0.043 1917 Dihedral : 6.542 71.899 1579 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 1.75 % Allowed : 14.07 % Favored : 84.18 % 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: -0.06 (0.23), residues: 1342 helix: 1.40 (0.22), residues: 565 sheet: 0.30 (0.37), residues: 194 loop : -1.67 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.010 0.001 HIS A 716 PHE 0.016 0.001 PHE A 633 TYR 0.014 0.001 TYR A 324 ARG 0.012 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 3) link_NAG-ASN : angle 3.60298 ( 9) link_ALPHA1-3 : bond 0.00526 ( 1) link_ALPHA1-3 : angle 1.86948 ( 3) hydrogen bonds : bond 0.03813 ( 476) hydrogen bonds : angle 4.38509 ( 1353) SS BOND : bond 0.00777 ( 3) SS BOND : angle 1.65947 ( 6) link_BETA1-3 : bond 0.00348 ( 1) link_BETA1-3 : angle 2.91832 ( 3) covalent geometry : bond 0.00264 (11243) covalent geometry : angle 0.51425 (15232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.356 Fit side-chains REVERT: A 145 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8251 (p0) REVERT: A 193 THR cc_start: 0.8328 (p) cc_final: 0.7898 (p) REVERT: A 252 LYS cc_start: 0.8042 (tppt) cc_final: 0.7130 (tmtt) REVERT: A 258 TYR cc_start: 0.8204 (m-10) cc_final: 0.7848 (m-10) REVERT: A 419 MET cc_start: 0.7012 (mmt) cc_final: 0.6803 (mmt) REVERT: A 596 LEU cc_start: 0.7505 (mp) cc_final: 0.7288 (mp) REVERT: A 629 MET cc_start: 0.6793 (mmt) cc_final: 0.6530 (mmt) REVERT: A 631 LYS cc_start: 0.7419 (ttpt) cc_final: 0.6662 (mtmt) REVERT: A 678 MET cc_start: 0.8311 (tmm) cc_final: 0.7988 (tmm) REVERT: A 942 TYR cc_start: 0.7867 (m-80) cc_final: 0.7526 (m-80) REVERT: A 943 MET cc_start: 0.8239 (tpt) cc_final: 0.5971 (tpt) outliers start: 21 outliers final: 17 residues processed: 135 average time/residue: 0.2289 time to fit residues: 45.4649 Evaluate side-chains 131 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 16 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118677 restraints weight = 14408.672| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.31 r_work: 0.3113 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11251 Z= 0.161 Angle : 0.564 7.312 15253 Z= 0.289 Chirality : 0.044 0.196 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.640 72.351 1579 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.83 % Allowed : 14.15 % Favored : 84.01 % 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: -0.14 (0.23), residues: 1342 helix: 1.29 (0.22), residues: 567 sheet: 0.35 (0.36), residues: 197 loop : -1.73 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.009 0.001 HIS A 716 PHE 0.019 0.002 PHE A 462 TYR 0.013 0.001 TYR A 324 ARG 0.002 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 3) link_NAG-ASN : angle 3.56720 ( 9) link_ALPHA1-3 : bond 0.00448 ( 1) link_ALPHA1-3 : angle 2.06216 ( 3) hydrogen bonds : bond 0.04176 ( 476) hydrogen bonds : angle 4.45587 ( 1353) SS BOND : bond 0.01093 ( 3) SS BOND : angle 1.54093 ( 6) link_BETA1-3 : bond 0.00263 ( 1) link_BETA1-3 : angle 3.12336 ( 3) covalent geometry : bond 0.00380 (11243) covalent geometry : angle 0.55411 (15232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.235 Fit side-chains REVERT: A 145 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8275 (p0) REVERT: A 193 THR cc_start: 0.8346 (p) cc_final: 0.7922 (p) REVERT: A 252 LYS cc_start: 0.8045 (tppt) cc_final: 0.7123 (tmtt) REVERT: A 258 TYR cc_start: 0.8240 (m-10) cc_final: 0.7887 (m-10) REVERT: A 629 MET cc_start: 0.6737 (mmt) cc_final: 0.6479 (mmt) REVERT: A 631 LYS cc_start: 0.7398 (ttpt) cc_final: 0.6614 (mtmt) REVERT: A 678 MET cc_start: 0.8322 (tmm) cc_final: 0.7988 (tmm) REVERT: A 942 TYR cc_start: 0.7920 (m-80) cc_final: 0.7572 (m-80) outliers start: 22 outliers final: 19 residues processed: 134 average time/residue: 0.2363 time to fit residues: 46.4385 Evaluate side-chains 133 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 127 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.154357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119714 restraints weight = 14273.012| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.26 r_work: 0.3130 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11251 Z= 0.139 Angle : 0.548 7.000 15253 Z= 0.281 Chirality : 0.043 0.185 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.565 72.306 1579 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.75 % Allowed : 14.07 % Favored : 84.18 % 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: -0.11 (0.23), residues: 1342 helix: 1.34 (0.22), residues: 565 sheet: 0.33 (0.36), residues: 198 loop : -1.71 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.009 0.001 HIS A 716 PHE 0.018 0.001 PHE A 633 TYR 0.014 0.001 TYR A 324 ARG 0.010 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 3) link_NAG-ASN : angle 3.56672 ( 9) link_ALPHA1-3 : bond 0.00447 ( 1) link_ALPHA1-3 : angle 1.92925 ( 3) hydrogen bonds : bond 0.04037 ( 476) hydrogen bonds : angle 4.41910 ( 1353) SS BOND : bond 0.00872 ( 3) SS BOND : angle 1.22266 ( 6) link_BETA1-3 : bond 0.00285 ( 1) link_BETA1-3 : angle 3.10263 ( 3) covalent geometry : bond 0.00326 (11243) covalent geometry : angle 0.53878 (15232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.236 Fit side-chains REVERT: A 145 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8250 (p0) REVERT: A 193 THR cc_start: 0.8330 (p) cc_final: 0.7908 (p) REVERT: A 252 LYS cc_start: 0.8040 (tppt) cc_final: 0.7120 (tmtt) REVERT: A 258 TYR cc_start: 0.8224 (m-10) cc_final: 0.7861 (m-10) REVERT: A 629 MET cc_start: 0.6725 (mmt) cc_final: 0.6481 (mmt) REVERT: A 631 LYS cc_start: 0.7406 (ttpt) cc_final: 0.6593 (mtmt) REVERT: A 678 MET cc_start: 0.8323 (tmm) cc_final: 0.7997 (tmm) REVERT: A 942 TYR cc_start: 0.7855 (m-80) cc_final: 0.7552 (m-80) outliers start: 21 outliers final: 19 residues processed: 128 average time/residue: 0.2278 time to fit residues: 42.6687 Evaluate side-chains 128 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 88 optimal weight: 0.0050 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.7254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121773 restraints weight = 14152.960| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.03 r_work: 0.3182 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11251 Z= 0.104 Angle : 0.522 7.536 15253 Z= 0.266 Chirality : 0.042 0.194 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.374 71.820 1579 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.50 % Allowed : 14.32 % Favored : 84.18 % 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: 0.10 (0.23), residues: 1342 helix: 1.52 (0.22), residues: 564 sheet: 0.50 (0.37), residues: 190 loop : -1.60 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.010 0.001 HIS A 716 PHE 0.015 0.001 PHE A 633 TYR 0.015 0.001 TYR A 324 ARG 0.009 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 3) link_NAG-ASN : angle 3.59229 ( 9) link_ALPHA1-3 : bond 0.00508 ( 1) link_ALPHA1-3 : angle 1.71969 ( 3) hydrogen bonds : bond 0.03619 ( 476) hydrogen bonds : angle 4.26968 ( 1353) SS BOND : bond 0.00720 ( 3) SS BOND : angle 1.01534 ( 6) link_BETA1-3 : bond 0.00434 ( 1) link_BETA1-3 : angle 2.91084 ( 3) covalent geometry : bond 0.00231 (11243) covalent geometry : angle 0.51206 (15232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6428.27 seconds wall clock time: 111 minutes 41.92 seconds (6701.92 seconds total)