Starting phenix.real_space_refine on Sat Jun 14 17:55:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8t_44358/06_2025/9b8t_44358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8t_44358/06_2025/9b8t_44358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8t_44358/06_2025/9b8t_44358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8t_44358/06_2025/9b8t_44358.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8t_44358/06_2025/9b8t_44358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8t_44358/06_2025/9b8t_44358.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 Fe 4 7.16 5 P 53 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 10221 2.51 5 N 2766 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16399 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9313 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 58, 'TRANS': 1087} Chain breaks: 1 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'SF4': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4940 SG CYS A 663 70.973 79.154 48.069 1.00 72.87 S ATOM 4874 SG CYS A 654 75.834 75.266 45.585 1.00 88.21 S ATOM 5664 SG CYS A 747 69.867 73.512 46.501 1.00 39.67 S ATOM 4858 SG CYS A 651 72.585 74.287 51.633 1.00 72.97 S Time building chain proxies: 10.58, per 1000 atoms: 0.65 Number of scatterers: 16399 At special positions: 0 Unit cell: (101.016, 109.296, 144.9, 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) Fe 4 26.01 S 102 16.00 P 53 15.00 Mg 1 11.99 O 3252 8.00 N 2766 7.00 C 10221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A3003 " pdb="FE3 SF4 A3003 " - pdb=" SG CYS A 747 " pdb="FE1 SF4 A3003 " - pdb=" SG CYS A 663 " pdb="FE2 SF4 A3003 " - pdb=" SG CYS A 654 " pdb="FE4 SF4 A3003 " - pdb=" SG CYS A 651 " Number of angles added : 12 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 33.4% alpha, 23.7% beta 22 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 7.04 Creating SS restraints... Processing helix chain 'A' and resid 24 through 48 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 159 through 180 Proline residue: A 172 - end of helix removed outlier: 3.609A pdb=" N LYS A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.706A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 407 through 415 removed outlier: 4.323A pdb=" N ARG A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 423 through 431 removed outlier: 4.765A pdb=" N LYS A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 474 removed outlier: 3.759A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 563 through 584 removed outlier: 4.113A pdb=" N PHE A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 576 " --> pdb=" O GLN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.175A pdb=" N LEU A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 647 through 654 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.774A pdb=" N ARG A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 726 " --> pdb=" O ARG A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 783 Processing helix chain 'A' and resid 790 through 818 removed outlier: 3.906A pdb=" N ILE A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 828 through 851 removed outlier: 4.596A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY A 833 " --> pdb=" O MET A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 905 Processing helix chain 'A' and resid 980 through 989 Processing helix chain 'A' and resid 990 through 995 removed outlier: 3.883A pdb=" N LEU A 994 " --> pdb=" O GLU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.862A pdb=" N GLY A1047 " --> pdb=" O GLU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1089 through 1091 No H-bonds generated for 'chain 'A' and resid 1089 through 1091' Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1106 through 1114 removed outlier: 4.367A pdb=" N TRP A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.969A pdb=" N ILE A1127 " --> pdb=" O ASP A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1176 removed outlier: 3.537A pdb=" N ASP A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'B' and resid 9 through 21 removed outlier: 4.004A pdb=" N LYS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.581A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.783A pdb=" N ARG C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.784A pdb=" N THR C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.695A pdb=" N LYS D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.635A pdb=" N ILE D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 209 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.658A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.658A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A 85 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP A 243 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 136 removed outlier: 3.751A pdb=" N LYS A 130 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 132 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 104 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP A 220 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.022A pdb=" N LEU A 272 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET A 359 " --> pdb=" O MET A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 278 removed outlier: 3.655A pdb=" N MET A 295 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.657A pdb=" N TRP A 865 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU A 859 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE A 622 " --> pdb=" O PRO A 936 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS A 624 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.919A pdb=" N ALA A 939 " --> pdb=" O PHE A 959 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AB1, first strand: chain 'A' and resid 645 through 646 Processing sheet with id=AB2, first strand: chain 'A' and resid 876 through 879 Processing sheet with id=AB3, first strand: chain 'A' and resid 911 through 913 Processing sheet with id=AB4, first strand: chain 'A' and resid 978 through 979 removed outlier: 3.718A pdb=" N ASN A1036 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1189 through 1192 Processing sheet with id=AB6, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.782A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 3 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 116 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.471A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.218A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 59 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.885A pdb=" N SER D 172 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 66 through 71 removed outlier: 3.628A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 29 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 36 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 51 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS C 246 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 237 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 67 through 68 removed outlier: 5.462A pdb=" N SER D 230 " --> pdb=" O PRO D 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 228 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 10.14 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 6711 1.40 - 1.62: 9942 1.62 - 1.84: 158 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 16823 Sorted by residual: bond pdb=" C PRO A 452 " pdb=" O PRO A 452 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.16e-02 7.43e+03 2.73e+01 bond pdb=" C GLN A 451 " pdb=" O GLN A 451 " ideal model delta sigma weight residual 1.238 1.292 -0.054 1.28e-02 6.10e+03 1.78e+01 bond pdb=" N ASP A 462 " pdb=" CA ASP A 462 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.44e-02 4.82e+03 8.56e+00 bond pdb=" N ILE D 11 " pdb=" CA ILE D 11 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.99e+00 bond pdb=" N ARG A1111 " pdb=" CA ARG A1111 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.52e+00 ... (remaining 16818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 22504 2.92 - 5.84: 374 5.84 - 8.76: 56 8.76 - 11.68: 16 11.68 - 14.60: 2 Bond angle restraints: 22952 Sorted by residual: angle pdb=" CB MET C 244 " pdb=" CG MET C 244 " pdb=" SD MET C 244 " ideal model delta sigma weight residual 112.70 127.30 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CA GLU A 36 " pdb=" CB GLU A 36 " pdb=" CG GLU A 36 " ideal model delta sigma weight residual 114.10 123.78 -9.68 2.00e+00 2.50e-01 2.34e+01 angle pdb=" CA GLU A1173 " pdb=" CB GLU A1173 " pdb=" CG GLU A1173 " ideal model delta sigma weight residual 114.10 123.02 -8.92 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB ARG A 154 " pdb=" CG ARG A 154 " pdb=" CD ARG A 154 " ideal model delta sigma weight residual 111.30 121.51 -10.21 2.30e+00 1.89e-01 1.97e+01 angle pdb=" N VAL A 785 " pdb=" CA VAL A 785 " pdb=" C VAL A 785 " ideal model delta sigma weight residual 108.65 102.25 6.40 1.45e+00 4.76e-01 1.95e+01 ... (remaining 22947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 9302 28.46 - 56.91: 792 56.91 - 85.37: 64 85.37 - 113.83: 3 113.83 - 142.29: 3 Dihedral angle restraints: 10164 sinusoidal: 4501 harmonic: 5663 Sorted by residual: dihedral pdb=" C2 TTP A3001 " pdb=" C1' TTP A3001 " pdb=" N1 TTP A3001 " pdb=" O4' TTP A3001 " ideal model delta sinusoidal sigma weight residual 301.68 159.40 142.29 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" O3A TTP A3001 " pdb=" O3B TTP A3001 " pdb=" PB TTP A3001 " pdb=" PG TTP A3001 " ideal model delta sinusoidal sigma weight residual 179.98 -53.61 -126.41 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" O5' TTP A3001 " pdb=" O3A TTP A3001 " pdb=" PA TTP A3001 " pdb=" PB TTP A3001 " ideal model delta sinusoidal sigma weight residual 180.02 54.81 125.21 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 10161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2201 0.077 - 0.154: 330 0.154 - 0.231: 23 0.231 - 0.308: 2 0.308 - 0.385: 1 Chirality restraints: 2557 Sorted by residual: chirality pdb=" CB VAL A 785 " pdb=" CA VAL A 785 " pdb=" CG1 VAL A 785 " pdb=" CG2 VAL A 785 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CG LEU A 272 " pdb=" CB LEU A 272 " pdb=" CD1 LEU A 272 " pdb=" CD2 LEU A 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CG LEU A 897 " pdb=" CB LEU A 897 " pdb=" CD1 LEU A 897 " pdb=" CD2 LEU A 897 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2554 not shown) Planarity restraints: 2781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 450 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C GLU A 450 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU A 450 " 0.032 2.00e-02 2.50e+03 pdb=" N GLN A 451 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 516 " 0.035 2.00e-02 2.50e+03 3.36e-02 1.98e+01 pdb=" CG PHE A 516 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE A 516 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 516 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 516 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 516 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 516 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " -0.022 2.00e-02 2.50e+03 2.18e-02 9.49e+00 pdb=" CG TYR A 103 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 ... (remaining 2778 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 220 2.65 - 3.21: 13288 3.21 - 3.77: 26847 3.77 - 4.34: 35556 4.34 - 4.90: 57169 Nonbonded interactions: 133080 Sorted by model distance: nonbonded pdb=" O VAL A 627 " pdb="MG MG A3002 " model vdw 2.085 2.170 nonbonded pdb=" O1G TTP A3001 " pdb="MG MG A3002 " model vdw 2.200 2.170 nonbonded pdb=" OH TYR A 754 " pdb=" O PHE A 815 " model vdw 2.278 3.040 nonbonded pdb=" O GLU B 25 " pdb=" OG SER B 39 " model vdw 2.292 3.040 nonbonded pdb=" OG SER D 43 " pdb=" OH TYR D 211 " model vdw 2.299 3.040 ... (remaining 133075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 55.190 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 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:17.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 0.071 16827 Z= 0.255 Angle : 0.988 17.015 22964 Z= 0.520 Chirality : 0.054 0.385 2557 Planarity : 0.007 0.066 2781 Dihedral : 18.825 142.286 6494 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.30 % Allowed : 25.52 % Favored : 70.18 % 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: -1.97 (0.17), residues: 1919 helix: -1.26 (0.19), residues: 571 sheet: -0.39 (0.23), residues: 506 loop : -1.85 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 28 HIS 0.010 0.001 HIS A 350 PHE 0.076 0.003 PHE A 516 TYR 0.054 0.003 TYR A 103 ARG 0.017 0.001 ARG A 728 Details of bonding type rmsd hydrogen bonds : bond 0.18624 ( 788) hydrogen bonds : angle 7.72100 ( 2186) metal coordination : bond 0.00847 ( 4) metal coordination : angle 10.71549 ( 12) covalent geometry : bond 0.00503 (16823) covalent geometry : angle 0.95698 (22952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 225 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7348 (tm) cc_final: 0.7123 (mp) REVERT: A 221 MET cc_start: 0.7315 (mpt) cc_final: 0.6725 (ptt) REVERT: A 295 MET cc_start: 0.5927 (mtm) cc_final: 0.5693 (mmt) REVERT: A 715 GLN cc_start: 0.6378 (mt0) cc_final: 0.5876 (mm-40) REVERT: A 1083 LYS cc_start: 0.5645 (mmmt) cc_final: 0.5133 (mttt) REVERT: B 94 ASP cc_start: 0.3752 (m-30) cc_final: 0.3028 (p0) REVERT: B 197 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6447 (pt) REVERT: B 217 LYS cc_start: 0.6445 (mmmm) cc_final: 0.6200 (mmtt) REVERT: B 246 HIS cc_start: 0.6286 (p90) cc_final: 0.6081 (p90) REVERT: C 1 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5196 (ttm) REVERT: C 244 MET cc_start: 0.7148 (tpp) cc_final: 0.6740 (ttm) REVERT: D 179 ASN cc_start: 0.7406 (p0) cc_final: 0.6959 (p0) REVERT: D 244 MET cc_start: 0.4896 (tpp) cc_final: 0.4599 (tpp) outliers start: 73 outliers final: 39 residues processed: 272 average time/residue: 1.1248 time to fit residues: 346.9908 Evaluate side-chains 234 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 8.9990 chunk 148 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 394 GLN A 475 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.235435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.206508 restraints weight = 19589.925| |-----------------------------------------------------------------------------| r_work (start): 0.4604 rms_B_bonded: 2.86 r_work: 0.4226 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16827 Z= 0.139 Angle : 0.648 16.155 22964 Z= 0.320 Chirality : 0.043 0.160 2557 Planarity : 0.005 0.046 2781 Dihedral : 15.676 140.389 2732 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.77 % Allowed : 23.16 % Favored : 71.07 % 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: -1.19 (0.18), residues: 1919 helix: -0.22 (0.20), residues: 577 sheet: -0.22 (0.23), residues: 510 loop : -1.49 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 28 HIS 0.004 0.001 HIS A 229 PHE 0.035 0.002 PHE C 215 TYR 0.014 0.002 TYR A 468 ARG 0.005 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 788) hydrogen bonds : angle 5.71157 ( 2186) metal coordination : bond 0.01096 ( 4) metal coordination : angle 9.85666 ( 12) covalent geometry : bond 0.00308 (16823) covalent geometry : angle 0.60753 (22952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 208 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 THR cc_start: 0.6755 (m) cc_final: 0.6388 (t) REVERT: A 46 LEU cc_start: 0.7194 (tm) cc_final: 0.6992 (mp) REVERT: A 151 ASN cc_start: 0.5201 (p0) cc_final: 0.4595 (m-40) REVERT: A 715 GLN cc_start: 0.6595 (mt0) cc_final: 0.6167 (mm-40) REVERT: A 921 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.5030 (m-80) REVERT: A 1030 PHE cc_start: 0.6235 (t80) cc_final: 0.6004 (t80) REVERT: A 1189 LEU cc_start: 0.7679 (mp) cc_final: 0.7443 (pp) REVERT: B 94 ASP cc_start: 0.3739 (m-30) cc_final: 0.3089 (p0) REVERT: B 116 MET cc_start: 0.5249 (OUTLIER) cc_final: 0.5023 (ptm) REVERT: B 197 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6671 (pt) REVERT: C 1 MET cc_start: 0.6264 (mmt) cc_final: 0.5209 (ttm) REVERT: C 216 THR cc_start: 0.5494 (OUTLIER) cc_final: 0.5126 (p) REVERT: D 138 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7205 (tmtt) REVERT: D 179 ASN cc_start: 0.7102 (p0) cc_final: 0.6871 (p0) outliers start: 98 outliers final: 35 residues processed: 279 average time/residue: 1.0574 time to fit residues: 337.6158 Evaluate side-chains 228 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 988 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 138 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 177 ASN ** A 229 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 = 0.4820 r_free = 0.4820 target = 0.230497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.207877 restraints weight = 19315.461| |-----------------------------------------------------------------------------| r_work (start): 0.4623 rms_B_bonded: 2.36 r_work: 0.4160 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16827 Z= 0.187 Angle : 0.685 16.169 22964 Z= 0.337 Chirality : 0.044 0.168 2557 Planarity : 0.005 0.038 2781 Dihedral : 15.584 135.120 2686 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.19 % Allowed : 23.57 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 1919 helix: -0.06 (0.21), residues: 593 sheet: -0.11 (0.23), residues: 510 loop : -1.48 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 40 HIS 0.013 0.001 HIS A 229 PHE 0.022 0.002 PHE C 215 TYR 0.024 0.002 TYR A 631 ARG 0.008 0.001 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 788) hydrogen bonds : angle 5.59365 ( 2186) metal coordination : bond 0.01074 ( 4) metal coordination : angle 9.92940 ( 12) covalent geometry : bond 0.00421 (16823) covalent geometry : angle 0.64690 (22952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 211 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5573 (mmm160) cc_final: 0.4598 (mmp80) REVERT: A 151 ASN cc_start: 0.5221 (p0) cc_final: 0.4555 (m-40) REVERT: A 299 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6403 (mtm) REVERT: A 715 GLN cc_start: 0.6715 (mt0) cc_final: 0.6420 (mm-40) REVERT: B 94 ASP cc_start: 0.3697 (m-30) cc_final: 0.3118 (OUTLIER) REVERT: B 116 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.5104 (ptm) REVERT: B 197 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6681 (pt) REVERT: B 204 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7062 (pp30) REVERT: C 1 MET cc_start: 0.6154 (mmt) cc_final: 0.5475 (ttm) REVERT: C 41 ASP cc_start: 0.5450 (t0) cc_final: 0.5032 (t0) REVERT: C 159 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.6998 (m) REVERT: D 138 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7538 (tmtt) outliers start: 105 outliers final: 48 residues processed: 287 average time/residue: 0.9723 time to fit residues: 320.7058 Evaluate side-chains 239 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 988 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 21 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 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 = 0.4830 r_free = 0.4830 target = 0.231818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.202612 restraints weight = 19379.170| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 2.84 r_work: 0.4183 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16827 Z= 0.146 Angle : 0.640 15.315 22964 Z= 0.314 Chirality : 0.043 0.159 2557 Planarity : 0.004 0.040 2781 Dihedral : 15.457 137.779 2685 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.07 % Allowed : 24.04 % Favored : 69.89 % 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: -0.93 (0.18), residues: 1919 helix: 0.12 (0.21), residues: 596 sheet: -0.02 (0.23), residues: 506 loop : -1.51 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 28 HIS 0.011 0.001 HIS A 229 PHE 0.043 0.002 PHE C 215 TYR 0.022 0.002 TYR C 249 ARG 0.004 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 788) hydrogen bonds : angle 5.39376 ( 2186) metal coordination : bond 0.00756 ( 4) metal coordination : angle 9.24722 ( 12) covalent geometry : bond 0.00331 (16823) covalent geometry : angle 0.60462 (22952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 203 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7037 (tm) cc_final: 0.6780 (mp) REVERT: A 151 ASN cc_start: 0.5221 (p0) cc_final: 0.4657 (m-40) REVERT: A 299 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6406 (mtm) REVERT: A 446 ARG cc_start: 0.2016 (OUTLIER) cc_final: 0.1599 (mmp-170) REVERT: A 574 VAL cc_start: 0.6264 (OUTLIER) cc_final: 0.6026 (t) REVERT: A 715 GLN cc_start: 0.6604 (mt0) cc_final: 0.6279 (mm-40) REVERT: A 878 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: A 921 TYR cc_start: 0.5899 (OUTLIER) cc_final: 0.5171 (m-80) REVERT: A 1189 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7243 (pp) REVERT: B 47 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7017 (tp) REVERT: B 94 ASP cc_start: 0.3471 (m-30) cc_final: 0.3111 (p0) REVERT: B 116 MET cc_start: 0.4957 (OUTLIER) cc_final: 0.4730 (ptm) REVERT: B 197 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6669 (pt) REVERT: B 204 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6975 (pp30) REVERT: C 41 ASP cc_start: 0.5568 (t0) cc_final: 0.5108 (t0) REVERT: C 159 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.7093 (m) outliers start: 103 outliers final: 44 residues processed: 272 average time/residue: 1.0117 time to fit residues: 314.9786 Evaluate side-chains 236 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 133 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 0.0270 chunk 90 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 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 = 0.4835 r_free = 0.4835 target = 0.232650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.202383 restraints weight = 19617.383| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 2.98 r_work: 0.4210 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16827 Z= 0.135 Angle : 0.629 14.191 22964 Z= 0.308 Chirality : 0.042 0.156 2557 Planarity : 0.004 0.037 2781 Dihedral : 15.377 138.131 2685 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.60 % Allowed : 25.22 % Favored : 69.18 % 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: -0.75 (0.19), residues: 1919 helix: 0.28 (0.21), residues: 594 sheet: 0.05 (0.23), residues: 521 loop : -1.40 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 40 HIS 0.010 0.001 HIS A 229 PHE 0.040 0.002 PHE C 215 TYR 0.019 0.002 TYR A 397 ARG 0.005 0.000 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 788) hydrogen bonds : angle 5.24457 ( 2186) metal coordination : bond 0.00619 ( 4) metal coordination : angle 8.52848 ( 12) covalent geometry : bond 0.00309 (16823) covalent geometry : angle 0.59862 (22952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 196 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.5185 (OUTLIER) cc_final: 0.4724 (m-40) REVERT: A 299 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6265 (mtm) REVERT: A 446 ARG cc_start: 0.2207 (OUTLIER) cc_final: 0.1590 (mmp-170) REVERT: A 732 LYS cc_start: 0.6494 (mmtm) cc_final: 0.6234 (mmtm) REVERT: A 878 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: B 47 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6988 (tp) REVERT: B 116 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4961 (ptm) REVERT: B 197 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6702 (pt) REVERT: B 200 ASN cc_start: 0.5084 (m110) cc_final: 0.4879 (m110) REVERT: B 204 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6828 (pp30) REVERT: C 1 MET cc_start: 0.5892 (mmm) cc_final: 0.5293 (mmt) REVERT: C 41 ASP cc_start: 0.5488 (t0) cc_final: 0.5006 (t0) REVERT: C 159 VAL cc_start: 0.7192 (OUTLIER) cc_final: 0.6973 (m) outliers start: 95 outliers final: 48 residues processed: 263 average time/residue: 1.0899 time to fit residues: 329.5606 Evaluate side-chains 240 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 172 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 156 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 150 optimal weight: 0.0980 chunk 163 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.233693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.204341 restraints weight = 19655.644| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 2.95 r_work: 0.4205 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16827 Z= 0.128 Angle : 0.635 13.193 22964 Z= 0.309 Chirality : 0.043 0.195 2557 Planarity : 0.004 0.037 2781 Dihedral : 15.284 139.440 2678 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.07 % Allowed : 26.46 % Favored : 68.47 % 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: -0.65 (0.19), residues: 1919 helix: 0.34 (0.21), residues: 603 sheet: 0.14 (0.23), residues: 498 loop : -1.34 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1166 HIS 0.010 0.001 HIS A 229 PHE 0.039 0.001 PHE C 215 TYR 0.022 0.002 TYR A 468 ARG 0.006 0.000 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 788) hydrogen bonds : angle 5.17424 ( 2186) metal coordination : bond 0.00492 ( 4) metal coordination : angle 8.05672 ( 12) covalent geometry : bond 0.00291 (16823) covalent geometry : angle 0.60786 (22952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 210 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5789 (mmp80) cc_final: 0.5335 (mmp80) REVERT: A 46 LEU cc_start: 0.6992 (tm) cc_final: 0.6731 (mp) REVERT: A 151 ASN cc_start: 0.5235 (p0) cc_final: 0.4860 (m-40) REVERT: A 299 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6329 (mtm) REVERT: A 396 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: A 446 ARG cc_start: 0.2008 (OUTLIER) cc_final: 0.1719 (mmp-170) REVERT: A 468 TYR cc_start: 0.6209 (m-80) cc_final: 0.5977 (m-80) REVERT: A 732 LYS cc_start: 0.6393 (mmtm) cc_final: 0.6134 (mmtm) REVERT: A 878 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6710 (m-10) REVERT: B 47 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7032 (tp) REVERT: B 116 MET cc_start: 0.5038 (OUTLIER) cc_final: 0.4793 (ptm) REVERT: B 197 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6762 (pt) REVERT: B 199 MET cc_start: 0.5304 (tmm) cc_final: 0.4775 (ttm) REVERT: B 200 ASN cc_start: 0.5586 (m110) cc_final: 0.5223 (m110) REVERT: B 204 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6997 (pp30) REVERT: C 1 MET cc_start: 0.5710 (mmm) cc_final: 0.5164 (mmt) REVERT: C 41 ASP cc_start: 0.5539 (t70) cc_final: 0.4989 (t0) REVERT: C 139 MET cc_start: 0.4922 (tmt) cc_final: 0.4440 (tmt) REVERT: C 146 ARG cc_start: 0.6028 (mmm160) cc_final: 0.5697 (tpt-90) outliers start: 86 outliers final: 46 residues processed: 271 average time/residue: 1.3097 time to fit residues: 404.8011 Evaluate side-chains 237 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 165 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 42 optimal weight: 0.5980 chunk 90 optimal weight: 0.0170 chunk 190 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 81 optimal weight: 0.0980 chunk 139 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN A1180 GLN B 8 GLN B 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.234574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.205209 restraints weight = 19621.541| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 2.83 r_work: 0.4228 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16827 Z= 0.123 Angle : 0.630 12.348 22964 Z= 0.308 Chirality : 0.042 0.174 2557 Planarity : 0.004 0.037 2781 Dihedral : 15.207 139.520 2675 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.83 % Allowed : 27.28 % Favored : 67.88 % 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: -0.57 (0.19), residues: 1919 helix: 0.45 (0.21), residues: 601 sheet: 0.18 (0.23), residues: 498 loop : -1.31 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1113 HIS 0.010 0.001 HIS A 229 PHE 0.034 0.001 PHE C 215 TYR 0.021 0.002 TYR A 248 ARG 0.006 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 788) hydrogen bonds : angle 5.11446 ( 2186) metal coordination : bond 0.00400 ( 4) metal coordination : angle 7.71871 ( 12) covalent geometry : bond 0.00280 (16823) covalent geometry : angle 0.60535 (22952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 205 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.6948 (tm) cc_final: 0.6695 (mp) REVERT: A 151 ASN cc_start: 0.5251 (OUTLIER) cc_final: 0.5049 (m-40) REVERT: A 299 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6303 (mtm) REVERT: A 396 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: A 446 ARG cc_start: 0.2014 (OUTLIER) cc_final: 0.1561 (mmp-170) REVERT: B 47 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7060 (tp) REVERT: B 118 LEU cc_start: 0.5041 (pt) cc_final: 0.4696 (pp) REVERT: B 197 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6735 (pt) REVERT: B 199 MET cc_start: 0.5350 (tmm) cc_final: 0.4878 (ttm) REVERT: B 200 ASN cc_start: 0.5568 (m110) cc_final: 0.5223 (m110) REVERT: B 204 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7120 (pp30) REVERT: C 41 ASP cc_start: 0.5499 (t70) cc_final: 0.5022 (t0) REVERT: C 146 ARG cc_start: 0.5937 (mmm160) cc_final: 0.5662 (tpt-90) REVERT: C 147 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5761 (mp) REVERT: D 16 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8427 (mt) outliers start: 82 outliers final: 44 residues processed: 260 average time/residue: 1.1245 time to fit residues: 334.6533 Evaluate side-chains 242 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 154 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.231222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.199254 restraints weight = 19406.043| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 3.46 r_work: 0.4130 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16827 Z= 0.152 Angle : 0.672 13.228 22964 Z= 0.324 Chirality : 0.043 0.177 2557 Planarity : 0.004 0.038 2781 Dihedral : 15.310 138.397 2674 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.01 % Allowed : 27.93 % Favored : 67.06 % 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: -0.64 (0.19), residues: 1919 helix: 0.34 (0.21), residues: 601 sheet: 0.17 (0.23), residues: 498 loop : -1.34 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 28 HIS 0.010 0.001 HIS A 229 PHE 0.054 0.002 PHE A 516 TYR 0.026 0.002 TYR A 397 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 788) hydrogen bonds : angle 5.15639 ( 2186) metal coordination : bond 0.00722 ( 4) metal coordination : angle 7.92792 ( 12) covalent geometry : bond 0.00349 (16823) covalent geometry : angle 0.64704 (22952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6043 (mmp80) cc_final: 0.5242 (mmp80) REVERT: A 299 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6504 (mtm) REVERT: A 396 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: A 446 ARG cc_start: 0.2019 (OUTLIER) cc_final: 0.1815 (mmp-170) REVERT: B 118 LEU cc_start: 0.5334 (pt) cc_final: 0.5017 (pp) REVERT: B 197 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6860 (pt) REVERT: B 204 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: C 1 MET cc_start: 0.5613 (mmm) cc_final: 0.5095 (mmt) REVERT: C 16 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6146 (mm) REVERT: C 41 ASP cc_start: 0.5845 (t70) cc_final: 0.5183 (t0) REVERT: C 126 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5847 (pp) REVERT: C 146 ARG cc_start: 0.6039 (mmm160) cc_final: 0.5609 (tpt-90) REVERT: C 147 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.5817 (mp) REVERT: D 16 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8444 (mt) outliers start: 85 outliers final: 50 residues processed: 264 average time/residue: 1.0465 time to fit residues: 314.7248 Evaluate side-chains 238 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 130 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.233817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.203087 restraints weight = 19515.339| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 3.36 r_work: 0.4155 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16827 Z= 0.142 Angle : 0.674 12.901 22964 Z= 0.327 Chirality : 0.043 0.211 2557 Planarity : 0.004 0.039 2781 Dihedral : 15.276 139.906 2674 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.54 % Allowed : 28.70 % Favored : 66.76 % 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: -0.65 (0.19), residues: 1919 helix: 0.35 (0.21), residues: 601 sheet: 0.15 (0.23), residues: 513 loop : -1.37 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 28 HIS 0.010 0.001 HIS A 229 PHE 0.039 0.002 PHE A 516 TYR 0.032 0.002 TYR A 631 ARG 0.012 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 788) hydrogen bonds : angle 5.14088 ( 2186) metal coordination : bond 0.00680 ( 4) metal coordination : angle 7.32301 ( 12) covalent geometry : bond 0.00328 (16823) covalent geometry : angle 0.65288 (22952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 196 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7000 (tm) cc_final: 0.6736 (mp) REVERT: A 276 ILE cc_start: 0.6100 (pp) cc_final: 0.5639 (pp) REVERT: A 396 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: A 446 ARG cc_start: 0.2121 (OUTLIER) cc_final: 0.1629 (mmp-170) REVERT: A 1189 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7399 (pp) REVERT: B 47 LEU cc_start: 0.7348 (tm) cc_final: 0.7101 (tp) REVERT: B 64 ARG cc_start: 0.5108 (pmm-80) cc_final: 0.4636 (ptt-90) REVERT: B 118 LEU cc_start: 0.5619 (pt) cc_final: 0.5245 (pp) REVERT: B 197 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6883 (pt) REVERT: B 200 ASN cc_start: 0.5226 (m110) cc_final: 0.4984 (m110) REVERT: B 204 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7143 (pp30) REVERT: C 1 MET cc_start: 0.5700 (mmm) cc_final: 0.5070 (mmt) REVERT: C 16 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6196 (mm) REVERT: C 126 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5929 (pp) REVERT: C 146 ARG cc_start: 0.5896 (mmm160) cc_final: 0.5534 (tpt-90) REVERT: C 147 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.5867 (mp) outliers start: 77 outliers final: 49 residues processed: 255 average time/residue: 1.0732 time to fit residues: 310.3459 Evaluate side-chains 240 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 114 optimal weight: 0.0000 chunk 65 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 0.0980 chunk 143 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 715 GLN B 8 GLN D 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.227870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.193698 restraints weight = 19422.751| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.88 r_work: 0.4126 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16827 Z= 0.206 Angle : 0.735 12.691 22964 Z= 0.361 Chirality : 0.046 0.235 2557 Planarity : 0.004 0.039 2781 Dihedral : 15.849 176.030 2674 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.07 % Allowed : 29.40 % Favored : 66.53 % 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: -0.85 (0.19), residues: 1919 helix: 0.08 (0.21), residues: 599 sheet: 0.04 (0.23), residues: 512 loop : -1.39 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 40 HIS 0.009 0.001 HIS A 229 PHE 0.049 0.002 PHE A 516 TYR 0.038 0.002 TYR A 397 ARG 0.008 0.001 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 788) hydrogen bonds : angle 5.36453 ( 2186) metal coordination : bond 0.01236 ( 4) metal coordination : angle 7.79223 ( 12) covalent geometry : bond 0.00477 (16823) covalent geometry : angle 0.71301 (22952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.5952 (pp) cc_final: 0.5557 (pp) REVERT: A 396 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6284 (mt-10) REVERT: A 446 ARG cc_start: 0.2095 (OUTLIER) cc_final: 0.1638 (mmp-170) REVERT: A 645 MET cc_start: 0.6489 (mpp) cc_final: 0.6266 (mpt) REVERT: B 28 TRP cc_start: 0.4931 (m100) cc_final: 0.4469 (m100) REVERT: B 64 ARG cc_start: 0.4960 (pmm-80) cc_final: 0.4533 (ptt-90) REVERT: B 118 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5212 (pp) REVERT: B 200 ASN cc_start: 0.5201 (m110) cc_final: 0.4936 (m110) REVERT: B 204 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7168 (pp30) REVERT: C 1 MET cc_start: 0.5694 (mmm) cc_final: 0.5043 (mmt) REVERT: C 16 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6240 (mm) REVERT: C 41 ASP cc_start: 0.6226 (t0) cc_final: 0.5498 (t0) REVERT: C 126 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6089 (pp) REVERT: C 146 ARG cc_start: 0.5983 (mmm160) cc_final: 0.5681 (tpt-90) REVERT: C 147 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5792 (mp) REVERT: C 184 GLN cc_start: 0.6456 (mm110) cc_final: 0.5879 (mm-40) outliers start: 69 outliers final: 48 residues processed: 254 average time/residue: 1.4041 time to fit residues: 407.3272 Evaluate side-chains 242 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.233269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.201852 restraints weight = 19498.403| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 2.56 r_work: 0.4179 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16827 Z= 0.144 Angle : 0.693 11.061 22964 Z= 0.340 Chirality : 0.044 0.205 2557 Planarity : 0.004 0.079 2781 Dihedral : 15.333 140.160 2672 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.54 % Allowed : 30.11 % Favored : 66.35 % 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: -0.79 (0.19), residues: 1919 helix: 0.14 (0.21), residues: 604 sheet: 0.08 (0.23), residues: 511 loop : -1.39 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A1166 HIS 0.009 0.001 HIS A 229 PHE 0.035 0.002 PHE A 516 TYR 0.028 0.002 TYR A 631 ARG 0.016 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 788) hydrogen bonds : angle 5.22673 ( 2186) metal coordination : bond 0.00658 ( 4) metal coordination : angle 6.60173 ( 12) covalent geometry : bond 0.00333 (16823) covalent geometry : angle 0.67644 (22952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10719.04 seconds wall clock time: 188 minutes 52.61 seconds (11332.61 seconds total)