Starting phenix.real_space_refine on Fri Jul 3 21:40:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8t_44358/07_2026/9b8t_44358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8t_44358/07_2026/9b8t_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_44358/07_2026/9b8t_44358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8t_44358/07_2026/9b8t_44358.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8t_44358/07_2026/9b8t_44358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8t_44358/07_2026/9b8t_44358.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.72, per 1000 atoms: 0.23 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: 1.33 Conformation dependent library (CDL) restraints added in 673.5 milliseconds 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: 2.14 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: 3.99 Time building geometry restraints manager: 1.80 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=" O3B TTP A3001 " pdb=" PG TTP A3001 " ideal model delta sigma weight residual 1.748 1.606 0.142 2.00e-02 2.50e+03 5.03e+01 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=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" O3A TTP A3001 " pdb=" PB TTP A3001 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 16818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 22478 2.92 - 5.84: 389 5.84 - 8.76: 65 8.76 - 11.68: 18 11.68 - 14.60: 2 Bond angle restraints: 22952 Sorted by residual: angle pdb=" O4' DC P 35 " pdb=" C4' DC P 35 " pdb=" C3' DC P 35 " ideal model delta sigma weight residual 106.00 102.71 3.29 6.00e-01 2.78e+00 3.00e+01 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 ... (remaining 22947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.93: 9144 25.93 - 51.86: 897 51.86 - 77.78: 137 77.78 - 103.71: 9 103.71 - 129.64: 1 Dihedral angle restraints: 10188 sinusoidal: 4525 harmonic: 5663 Sorted by residual: dihedral pdb=" CA GLY A 49 " pdb=" C GLY A 49 " pdb=" N PHE A 50 " pdb=" CA PHE A 50 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+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 184.45 54.81 129.64 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CA ILE A1145 " pdb=" C ILE A1145 " pdb=" N THR A1146 " pdb=" CA THR A1146 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 10185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2181 0.077 - 0.154: 348 0.154 - 0.231: 25 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.640 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 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 0.142 16827 Z= 0.323 Angle : 1.023 17.015 22964 Z= 0.575 Chirality : 0.055 0.385 2557 Planarity : 0.007 0.066 2781 Dihedral : 18.822 129.638 6518 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.017 0.001 ARG A 728 TYR 0.054 0.003 TYR A 103 PHE 0.076 0.003 PHE A 516 TRP 0.032 0.003 TRP B 28 HIS 0.010 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.32 (16823) covalent geometry : angle 0.99392 / 0.57 (22952) hydrogen bonds : bond 0.18624 / 12.12 ( 788) hydrogen bonds : angle 7.72100 / 5.39 ( 2186) metal coordination : bond 0.00847 / 0.55 ( 4) metal coordination : angle 10.71549 / 7.75 ( 12) *********************** 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 : 0.641 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: 0.4974 time to fit residues: 153.4685 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 : 0.606 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN A 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.236346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.206964 restraints weight = 19550.374| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 2.80 r_work: 0.4249 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16827 Z= 0.154 Angle : 0.687 17.289 22964 Z= 0.345 Chirality : 0.044 0.164 2557 Planarity : 0.005 0.044 2781 Dihedral : 15.795 116.322 2756 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.48 % Allowed : 24.10 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.18), residues: 1919 helix: -0.32 (0.20), residues: 570 sheet: -0.19 (0.22), residues: 510 loop : -1.60 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 149 TYR 0.015 0.002 TYR A 468 PHE 0.029 0.002 PHE C 215 TRP 0.015 0.002 TRP A 40 HIS 0.006 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (16823) covalent geometry : angle 0.64325 / 0.34 (22952) hydrogen bonds : bond 0.04722 / 3.12 ( 788) hydrogen bonds : angle 6.03426 / 4.17 ( 2186) metal coordination : bond 0.00769 / 0.50 ( 4) metal coordination : angle 10.61523 / 7.96 ( 12) *********************** 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 293 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.5160 (p0) cc_final: 0.4355 (m-40) REVERT: A 299 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6026 (mtm) REVERT: A 347 TRP cc_start: 0.7282 (OUTLIER) cc_final: 0.7011 (t60) REVERT: A 447 MET cc_start: 0.3199 (pmm) cc_final: 0.2855 (ptt) REVERT: A 715 GLN cc_start: 0.6603 (mt0) cc_final: 0.6157 (mm-40) REVERT: A 921 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.5048 (m-80) REVERT: A 1030 PHE cc_start: 0.6297 (t80) cc_final: 0.6011 (t80) REVERT: A 1189 LEU cc_start: 0.7648 (mp) cc_final: 0.7320 (pp) REVERT: B 94 ASP cc_start: 0.3874 (m-30) cc_final: 0.3176 (p0) REVERT: B 116 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4866 (ptm) REVERT: B 197 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6622 (pt) REVERT: B 229 MET cc_start: 0.7005 (ptm) cc_final: 0.6797 (ptp) REVERT: C 1 MET cc_start: 0.6258 (mmt) cc_final: 0.5292 (ttm) REVERT: C 216 THR cc_start: 0.5544 (OUTLIER) cc_final: 0.5233 (p) outliers start: 93 outliers final: 38 residues processed: 265 average time/residue: 0.4275 time to fit residues: 130.1913 Evaluate side-chains 230 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 347 TRP Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 549 SER 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 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 979 LEU 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 B residue 16 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 111 VAL 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 C residue 7 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 31 SER 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 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 102 VAL Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 189 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.228899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.207453 restraints weight = 19573.046| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 2.35 r_work: 0.4140 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16827 Z= 0.231 Angle : 0.765 21.865 22964 Z= 0.380 Chirality : 0.047 0.181 2557 Planarity : 0.005 0.073 2781 Dihedral : 15.856 113.807 2718 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.66 % Allowed : 23.81 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.18), residues: 1919 helix: -0.35 (0.20), residues: 586 sheet: -0.19 (0.22), residues: 523 loop : -1.61 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 749 TYR 0.027 0.003 TYR A 397 PHE 0.024 0.002 PHE A 768 TRP 0.019 0.003 TRP A 40 HIS 0.012 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (16823) covalent geometry : angle 0.71852 / 0.38 (22952) hydrogen bonds : bond 0.05196 / 3.44 ( 788) hydrogen bonds : angle 5.87900 / 4.07 ( 2186) metal coordination : bond 0.01692 / 1.06 ( 4) metal coordination : angle 11.53553 / 8.84 ( 12) *********************** 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 320 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 207 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 41 THR cc_start: 0.6730 (m) cc_final: 0.6461 (t) REVERT: A 46 LEU cc_start: 0.7094 (tm) cc_final: 0.6881 (tt) REVERT: A 220 ASP cc_start: 0.7011 (t0) cc_final: 0.6645 (t70) REVERT: A 299 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6486 (mtm) REVERT: A 447 MET cc_start: 0.3404 (pmm) cc_final: 0.3019 (ptt) REVERT: A 715 GLN cc_start: 0.6756 (mt0) cc_final: 0.6491 (mm-40) REVERT: A 821 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.4915 (ptm160) REVERT: A 921 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.5259 (m-80) REVERT: B 94 ASP cc_start: 0.3744 (m-30) cc_final: 0.3211 (p0) REVERT: B 229 MET cc_start: 0.6959 (ptm) cc_final: 0.6699 (ttt) REVERT: C 1 MET cc_start: 0.6205 (mmt) cc_final: 0.5598 (ttm) REVERT: C 41 ASP cc_start: 0.5580 (t0) cc_final: 0.5125 (t0) REVERT: D 124 GLU cc_start: 0.6450 (tp30) cc_final: 0.6198 (pt0) REVERT: D 138 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7494 (tmtt) REVERT: D 179 ASN cc_start: 0.7337 (p0) cc_final: 0.7132 (p0) outliers start: 113 outliers final: 58 residues processed: 287 average time/residue: 0.4251 time to fit residues: 140.5087 Evaluate side-chains 250 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 294 MET Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 422 HIS 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 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 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 821 ARG 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 921 TYR Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 951 LYS 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 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 47 LEU 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 199 MET 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 29 ASP 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 1 MET 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 114 TYR Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 221 LEU 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 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 chunk 39 optimal weight: 0.0570 chunk 143 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN ** B 184 GLN ** 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 = 0.4831 r_free = 0.4831 target = 0.232169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.203583 restraints weight = 19427.436| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 2.81 r_work: 0.4172 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1937 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 : 0.661 17.744 22964 Z= 0.327 Chirality : 0.043 0.164 2557 Planarity : 0.004 0.040 2781 Dihedral : 15.535 108.091 2711 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.77 % Allowed : 24.69 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 1919 helix: -0.03 (0.21), residues: 577 sheet: -0.16 (0.23), residues: 521 loop : -1.51 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 61 TYR 0.035 0.002 TYR A 631 PHE 0.024 0.002 PHE C 215 TRP 0.016 0.002 TRP A 40 HIS 0.010 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (16823) covalent geometry : angle 0.61885 / 0.33 (22952) hydrogen bonds : bond 0.04167 / 2.80 ( 788) hydrogen bonds : angle 5.59210 / 3.86 ( 2186) metal coordination : bond 0.00800 / 0.47 ( 4) metal coordination : angle 10.19930 / 7.82 ( 12) *********************** 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 298 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 200 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6072 (tpp-160) cc_final: 0.5362 (mmp80) REVERT: A 41 THR cc_start: 0.6711 (m) cc_final: 0.6407 (t) REVERT: A 46 LEU cc_start: 0.7031 (tm) cc_final: 0.6775 (mp) REVERT: A 151 ASN cc_start: 0.5062 (p0) cc_final: 0.4465 (m-40) REVERT: A 220 ASP cc_start: 0.7029 (t0) cc_final: 0.6412 (t70) REVERT: A 305 TYR cc_start: 0.5819 (m-10) cc_final: 0.5461 (m-10) REVERT: A 350 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5180 (t-170) REVERT: A 715 GLN cc_start: 0.6699 (mt0) cc_final: 0.6355 (mm-40) REVERT: A 831 MET cc_start: 0.7283 (tmt) cc_final: 0.7041 (tmt) REVERT: A 878 PHE cc_start: 0.7175 (m-10) cc_final: 0.6898 (m-10) REVERT: A 1030 PHE cc_start: 0.6205 (t80) cc_final: 0.5903 (t80) REVERT: B 94 ASP cc_start: 0.3518 (m-30) cc_final: 0.3082 (OUTLIER) REVERT: B 116 MET cc_start: 0.6025 (ptm) cc_final: 0.5723 (ptm) REVERT: B 199 MET cc_start: 0.4757 (OUTLIER) cc_final: 0.4323 (ptm) REVERT: B 204 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7021 (pp30) REVERT: B 229 MET cc_start: 0.6999 (ptm) cc_final: 0.6686 (ptp) REVERT: C 1 MET cc_start: 0.6177 (mmt) cc_final: 0.5415 (ttm) REVERT: D 138 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7350 (tmtt) outliers start: 98 outliers final: 50 residues processed: 268 average time/residue: 0.4329 time to fit residues: 133.6180 Evaluate side-chains 241 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 526 LYS 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 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 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 1 MET Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 111 VAL 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 199 MET Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 29 ASP 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 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 1 MET 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 138 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 137 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 154 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.228596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.206737 restraints weight = 19413.624| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 2.38 r_work: 0.4132 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16827 Z= 0.197 Angle : 0.708 16.515 22964 Z= 0.352 Chirality : 0.045 0.182 2557 Planarity : 0.005 0.041 2781 Dihedral : 15.634 107.435 2710 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 6.31 % Allowed : 24.75 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.18), residues: 1919 helix: -0.08 (0.21), residues: 583 sheet: -0.16 (0.23), residues: 521 loop : -1.59 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 61 TYR 0.049 0.003 TYR C 249 PHE 0.020 0.002 PHE A 761 TRP 0.017 0.002 TRP B 28 HIS 0.010 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (16823) covalent geometry : angle 0.66869 / 0.35 (22952) hydrogen bonds : bond 0.04649 / 3.11 ( 788) hydrogen bonds : angle 5.65255 / 3.92 ( 2186) metal coordination : bond 0.01340 / 0.78 ( 4) metal coordination : angle 10.13858 / 7.68 ( 12) *********************** 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 302 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 195 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 THR cc_start: 0.6759 (m) cc_final: 0.6506 (t) REVERT: A 151 ASN cc_start: 0.5084 (p0) cc_final: 0.4438 (m-40) REVERT: A 220 ASP cc_start: 0.7056 (t0) cc_final: 0.6491 (t70) REVERT: A 221 MET cc_start: 0.7583 (mpt) cc_final: 0.7367 (mpt) REVERT: A 278 THR cc_start: 0.5580 (OUTLIER) cc_final: 0.5366 (t) REVERT: A 295 MET cc_start: 0.5906 (mmt) cc_final: 0.5552 (mtt) REVERT: A 299 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6432 (mtm) REVERT: A 350 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5160 (t70) REVERT: A 447 MET cc_start: 0.3503 (pmm) cc_final: 0.3040 (tpp) REVERT: A 715 GLN cc_start: 0.6741 (mt0) cc_final: 0.6406 (mm-40) REVERT: A 821 ARG cc_start: 0.5344 (OUTLIER) cc_final: 0.5006 (ptm160) REVERT: A 1030 PHE cc_start: 0.6314 (t80) cc_final: 0.6052 (t80) REVERT: B 199 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.4187 (ptm) REVERT: B 204 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7070 (pp30) REVERT: B 229 MET cc_start: 0.6923 (ptm) cc_final: 0.6568 (ptp) REVERT: C 1 MET cc_start: 0.6272 (mmt) cc_final: 0.5559 (ttm) REVERT: C 159 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6995 (m) REVERT: D 119 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4820 (ppp) REVERT: D 138 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7520 (tmtt) outliers start: 107 outliers final: 60 residues processed: 273 average time/residue: 0.4380 time to fit residues: 137.7942 Evaluate side-chains 254 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 185 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 460 VAL 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 574 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 821 ARG 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 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 21 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 199 MET 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 7 VAL 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 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 C residue 249 TYR Chi-restraints excluded: chain D residue 1 MET 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 114 TYR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 138 LYS 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 183 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 125 optimal weight: 0.0030 chunk 104 optimal weight: 0.0170 chunk 132 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 102 optimal weight: 0.0070 chunk 188 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 overall best weight: 0.2446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.233542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.205700 restraints weight = 19413.809| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 2.79 r_work: 0.4198 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16827 Z= 0.123 Angle : 0.650 15.954 22964 Z= 0.320 Chirality : 0.043 0.172 2557 Planarity : 0.004 0.065 2781 Dihedral : 15.446 99.481 2708 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.83 % Allowed : 26.58 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 1919 helix: 0.08 (0.21), residues: 592 sheet: -0.09 (0.23), residues: 504 loop : -1.49 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 37 TYR 0.045 0.002 TYR C 249 PHE 0.028 0.002 PHE A 389 TRP 0.018 0.002 TRP A 40 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (16823) covalent geometry : angle 0.61398 / 0.32 (22952) hydrogen bonds : bond 0.03835 / 2.60 ( 788) hydrogen bonds : angle 5.40286 / 3.74 ( 2186) metal coordination : bond 0.01536 / 0.78 ( 4) metal coordination : angle 9.30111 / 7.05 ( 12) *********************** 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 286 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5759 (mmm160) cc_final: 0.4719 (mmp80) REVERT: A 41 THR cc_start: 0.6717 (m) cc_final: 0.6477 (t) REVERT: A 46 LEU cc_start: 0.6959 (tm) cc_final: 0.6725 (mp) REVERT: A 151 ASN cc_start: 0.4973 (p0) cc_final: 0.4495 (m-40) REVERT: A 220 ASP cc_start: 0.6864 (t0) cc_final: 0.6360 (t70) REVERT: A 295 MET cc_start: 0.5747 (mmt) cc_final: 0.5506 (mtt) REVERT: A 305 TYR cc_start: 0.5808 (m-10) cc_final: 0.5429 (m-10) REVERT: A 350 HIS cc_start: 0.5954 (OUTLIER) cc_final: 0.5272 (t-170) REVERT: A 446 ARG cc_start: 0.2097 (OUTLIER) cc_final: 0.1622 (mmp-170) REVERT: A 447 MET cc_start: 0.3310 (pmm) cc_final: 0.2878 (ptt) REVERT: A 1189 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7181 (pp) REVERT: B 199 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4387 (ptm) REVERT: B 204 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7147 (pp30) REVERT: B 229 MET cc_start: 0.6919 (ptm) cc_final: 0.6564 (ptp) REVERT: C 1 MET cc_start: 0.6297 (mmt) cc_final: 0.6069 (mmm) REVERT: C 159 VAL cc_start: 0.7292 (OUTLIER) cc_final: 0.7084 (m) REVERT: D 138 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7427 (tmtt) outliers start: 82 outliers final: 37 residues processed: 262 average time/residue: 0.4306 time to fit residues: 129.5385 Evaluate side-chains 226 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 350 HIS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 551 VAL 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 867 VAL Chi-restraints excluded: chain A residue 899 ILE 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 A residue 1189 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 31 SER 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 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 TYR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 163 optimal weight: 0.0970 chunk 69 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.234658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.211139 restraints weight = 19374.932| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 2.50 r_work: 0.4176 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16827 Z= 0.136 Angle : 0.651 14.936 22964 Z= 0.321 Chirality : 0.043 0.176 2557 Planarity : 0.004 0.045 2781 Dihedral : 15.375 95.796 2708 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.71 % Allowed : 26.69 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 1919 helix: 0.15 (0.21), residues: 593 sheet: -0.09 (0.23), residues: 511 loop : -1.44 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.042 0.002 TYR C 249 PHE 0.027 0.002 PHE A 389 TRP 0.018 0.002 TRP B 28 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16823) covalent geometry : angle 0.61830 / 0.32 (22952) hydrogen bonds : bond 0.03905 / 2.65 ( 788) hydrogen bonds : angle 5.36464 / 3.73 ( 2186) metal coordination : bond 0.00453 / 0.30 ( 4) metal coordination : angle 8.92892 / 6.74 ( 12) *********************** 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 271 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5815 (mmm160) cc_final: 0.4891 (mmp80) REVERT: A 41 THR cc_start: 0.6758 (m) cc_final: 0.6480 (t) REVERT: A 46 LEU cc_start: 0.6983 (tm) cc_final: 0.6781 (tt) REVERT: A 151 ASN cc_start: 0.5000 (p0) cc_final: 0.4587 (m-40) REVERT: A 220 ASP cc_start: 0.6918 (t0) cc_final: 0.6437 (t70) REVERT: A 221 MET cc_start: 0.7436 (mpt) cc_final: 0.7207 (mpm) REVERT: A 295 MET cc_start: 0.5693 (mmt) cc_final: 0.5471 (mtt) REVERT: A 299 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6263 (mtm) REVERT: A 350 HIS cc_start: 0.6034 (OUTLIER) cc_final: 0.5235 (t-170) REVERT: A 446 ARG cc_start: 0.2266 (OUTLIER) cc_final: 0.1798 (mmp-170) REVERT: A 447 MET cc_start: 0.3370 (pmm) cc_final: 0.2975 (ptt) REVERT: A 454 THR cc_start: 0.6849 (m) cc_final: 0.6533 (p) REVERT: A 981 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 1030 PHE cc_start: 0.6143 (t80) cc_final: 0.5864 (t80) REVERT: B 116 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.4770 (ptm) REVERT: B 199 MET cc_start: 0.4595 (OUTLIER) cc_final: 0.4070 (ptm) REVERT: B 204 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7372 (pp30) REVERT: B 229 MET cc_start: 0.6727 (ptm) cc_final: 0.6486 (ttt) REVERT: C 159 VAL cc_start: 0.7225 (OUTLIER) cc_final: 0.7022 (m) REVERT: D 16 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8346 (mt) REVERT: D 119 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.4572 (ppp) REVERT: D 138 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7450 (tmtt) outliers start: 80 outliers final: 43 residues processed: 245 average time/residue: 0.4515 time to fit residues: 127.1779 Evaluate side-chains 239 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 299 MET Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 551 VAL 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 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 981 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 A residue 1154 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 MET 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 31 SER 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 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 1 MET 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 119 MET Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 136 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 143 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN ** B 184 GLN ** 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 = 0.4838 r_free = 0.4838 target = 0.233224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.203755 restraints weight = 19482.870| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 2.98 r_work: 0.4172 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16827 Z= 0.155 Angle : 0.686 14.493 22964 Z= 0.336 Chirality : 0.044 0.196 2557 Planarity : 0.004 0.038 2781 Dihedral : 15.403 92.832 2702 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.60 % Allowed : 27.34 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 1919 helix: 0.24 (0.21), residues: 591 sheet: -0.04 (0.23), residues: 517 loop : -1.43 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.023 0.002 TYR A 248 PHE 0.026 0.002 PHE A 389 TRP 0.021 0.002 TRP B 28 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (16823) covalent geometry : angle 0.65519 / 0.34 (22952) hydrogen bonds : bond 0.04048 / 2.74 ( 788) hydrogen bonds : angle 5.38735 / 3.75 ( 2186) metal coordination : bond 0.00864 / 0.51 ( 4) metal coordination : angle 8.90333 / 6.69 ( 12) *********************** 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 273 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5730 (mmm160) cc_final: 0.4753 (mmp80) REVERT: A 41 THR cc_start: 0.6654 (m) cc_final: 0.6413 (t) REVERT: A 151 ASN cc_start: 0.5007 (p0) cc_final: 0.4578 (m-40) REVERT: A 220 ASP cc_start: 0.6918 (t0) cc_final: 0.6549 (t70) REVERT: A 299 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6319 (mtm) REVERT: A 446 ARG cc_start: 0.2145 (OUTLIER) cc_final: 0.1615 (mmp-170) REVERT: A 468 TYR cc_start: 0.6063 (m-80) cc_final: 0.5848 (m-80) REVERT: A 878 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: A 981 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6946 (tp) REVERT: A 1030 PHE cc_start: 0.6168 (t80) cc_final: 0.5844 (t80) REVERT: B 116 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4767 (ptm) REVERT: B 199 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.4163 (ptm) REVERT: B 204 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7322 (pp30) REVERT: B 229 MET cc_start: 0.6730 (ptm) cc_final: 0.6473 (ttt) REVERT: C 1 MET cc_start: 0.5855 (mmm) cc_final: 0.5391 (mmt) REVERT: C 139 MET cc_start: 0.5042 (tmt) cc_final: 0.4717 (tmm) REVERT: D 16 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (mt) REVERT: D 119 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.4654 (ppp) REVERT: D 138 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7444 (tmtt) REVERT: D 184 GLN cc_start: 0.5639 (mp10) cc_final: 0.4995 (tp40) outliers start: 78 outliers final: 45 residues processed: 251 average time/residue: 0.4357 time to fit residues: 125.7749 Evaluate side-chains 239 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 299 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 551 VAL 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 922 VAL Chi-restraints excluded: chain A residue 981 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 A residue 1154 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 MET 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 31 SER 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 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 1 MET 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 119 MET Chi-restraints excluded: chain D residue 138 LYS 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 159 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.231402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.203300 restraints weight = 19577.766| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 2.91 r_work: 0.4170 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16827 Z= 0.148 Angle : 0.688 14.101 22964 Z= 0.335 Chirality : 0.044 0.196 2557 Planarity : 0.004 0.038 2781 Dihedral : 15.383 89.291 2700 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.01 % Allowed : 28.52 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.19), residues: 1919 helix: 0.20 (0.21), residues: 592 sheet: -0.00 (0.23), residues: 517 loop : -1.43 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.023 0.002 TYR A 248 PHE 0.031 0.002 PHE A 876 TRP 0.023 0.002 TRP B 28 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16823) covalent geometry : angle 0.65862 / 0.33 (22952) hydrogen bonds : bond 0.03937 / 2.68 ( 788) hydrogen bonds : angle 5.35696 / 3.73 ( 2186) metal coordination : bond 0.00771 / 0.45 ( 4) metal coordination : angle 8.67362 / 6.53 ( 12) *********************** 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 259 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 191 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5703 (mmm160) cc_final: 0.4840 (mmp80) REVERT: A 41 THR cc_start: 0.6758 (m) cc_final: 0.6509 (t) REVERT: A 46 LEU cc_start: 0.6982 (tm) cc_final: 0.6759 (mp) REVERT: A 151 ASN cc_start: 0.4973 (p0) cc_final: 0.4592 (m-40) REVERT: A 220 ASP cc_start: 0.6930 (t0) cc_final: 0.6597 (t70) REVERT: A 221 MET cc_start: 0.7419 (mpt) cc_final: 0.7208 (mpt) REVERT: A 295 MET cc_start: 0.6101 (mtt) cc_final: 0.5785 (mmp) REVERT: A 299 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6269 (mtm) REVERT: A 446 ARG cc_start: 0.2388 (OUTLIER) cc_final: 0.1921 (mmp-170) REVERT: A 447 MET cc_start: 0.3440 (pmm) cc_final: 0.3000 (tpp) REVERT: A 468 TYR cc_start: 0.6082 (m-80) cc_final: 0.5798 (m-80) REVERT: A 981 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6930 (tp) REVERT: A 1024 MET cc_start: 0.6205 (tmm) cc_final: 0.5997 (tmt) REVERT: A 1030 PHE cc_start: 0.6109 (t80) cc_final: 0.5862 (t80) REVERT: B 47 LEU cc_start: 0.7349 (tm) cc_final: 0.7038 (tp) REVERT: B 116 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.4753 (ptm) REVERT: B 118 LEU cc_start: 0.5216 (pt) cc_final: 0.4889 (pp) REVERT: B 199 MET cc_start: 0.4684 (OUTLIER) cc_final: 0.4328 (ptm) REVERT: B 204 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7258 (pp30) REVERT: B 229 MET cc_start: 0.6665 (ptm) cc_final: 0.6434 (ttt) REVERT: C 1 MET cc_start: 0.6038 (mmm) cc_final: 0.5517 (mmt) REVERT: C 139 MET cc_start: 0.5021 (tmt) cc_final: 0.4789 (tmm) REVERT: D 16 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8428 (mt) REVERT: D 119 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4587 (ppp) REVERT: D 138 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7494 (tmtt) REVERT: D 184 GLN cc_start: 0.5406 (mp10) cc_final: 0.5199 (tp40) outliers start: 68 outliers final: 40 residues processed: 239 average time/residue: 0.4694 time to fit residues: 128.3592 Evaluate side-chains 240 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 299 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL 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 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 981 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 A residue 1154 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 31 SER 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 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 119 MET Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.231349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.198012 restraints weight = 19561.576| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 2.67 r_work: 0.4189 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2760 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= 0.173 Angle : 0.706 14.288 22964 Z= 0.346 Chirality : 0.045 0.254 2557 Planarity : 0.004 0.038 2781 Dihedral : 15.426 86.857 2699 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.83 % Allowed : 29.05 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 1919 helix: 0.08 (0.21), residues: 594 sheet: -0.03 (0.23), residues: 513 loop : -1.45 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 61 TYR 0.024 0.002 TYR A 397 PHE 0.038 0.002 PHE A 516 TRP 0.024 0.002 TRP B 28 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (16823) covalent geometry : angle 0.67786 / 0.35 (22952) hydrogen bonds : bond 0.04142 / 2.81 ( 788) hydrogen bonds : angle 5.44226 / 3.79 ( 2186) metal coordination : bond 0.01124 / 0.65 ( 4) metal coordination : angle 8.71677 / 6.56 ( 12) ********************** 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 259 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 THR cc_start: 0.6957 (m) cc_final: 0.6681 (t) REVERT: A 46 LEU cc_start: 0.7059 (tm) cc_final: 0.6857 (tt) REVERT: A 151 ASN cc_start: 0.4953 (p0) cc_final: 0.4566 (m-40) REVERT: A 220 ASP cc_start: 0.6964 (t0) cc_final: 0.6670 (t70) REVERT: A 221 MET cc_start: 0.7527 (mpt) cc_final: 0.7283 (mpm) REVERT: A 299 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6357 (mtm) REVERT: A 446 ARG cc_start: 0.2008 (OUTLIER) cc_final: 0.1693 (mmp-170) REVERT: A 447 MET cc_start: 0.3418 (pmm) cc_final: 0.3018 (tpp) REVERT: A 468 TYR cc_start: 0.6194 (m-80) cc_final: 0.5904 (m-80) REVERT: A 878 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: A 981 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6945 (tp) REVERT: A 1024 MET cc_start: 0.5989 (tmm) cc_final: 0.5741 (tmt) REVERT: B 16 LEU cc_start: 0.6528 (tp) cc_final: 0.6098 (tp) REVERT: B 116 MET cc_start: 0.4930 (OUTLIER) cc_final: 0.4698 (ptm) REVERT: B 118 LEU cc_start: 0.5126 (pt) cc_final: 0.4809 (pp) REVERT: B 199 MET cc_start: 0.4608 (OUTLIER) cc_final: 0.4153 (ptm) REVERT: B 204 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7348 (pp30) REVERT: B 229 MET cc_start: 0.6712 (ptm) cc_final: 0.6448 (ttt) REVERT: C 1 MET cc_start: 0.5896 (mmm) cc_final: 0.5442 (mmt) REVERT: C 139 MET cc_start: 0.4754 (tmt) cc_final: 0.4514 (tmm) REVERT: D 16 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8443 (mt) REVERT: D 119 MET cc_start: 0.5660 (OUTLIER) cc_final: 0.4755 (ppp) REVERT: D 138 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7513 (tmtt) outliers start: 65 outliers final: 46 residues processed: 240 average time/residue: 0.4927 time to fit residues: 134.9720 Evaluate side-chains 243 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 299 MET Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 545 GLU 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 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 981 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 A residue 1154 VAL Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 199 MET 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 31 SER 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 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 119 MET Chi-restraints excluded: chain D residue 138 LYS 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 89 optimal weight: 0.0270 chunk 39 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 86 optimal weight: 0.0040 chunk 173 optimal weight: 2.9990 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 715 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.235047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.206851 restraints weight = 19803.100| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 2.87 r_work: 0.4214 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2786 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= 0.131 Angle : 0.671 13.619 22964 Z= 0.332 Chirality : 0.043 0.157 2557 Planarity : 0.004 0.038 2781 Dihedral : 15.334 82.379 2699 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.42 % Allowed : 29.88 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.19), residues: 1919 helix: 0.22 (0.21), residues: 591 sheet: -0.02 (0.23), residues: 516 loop : -1.43 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 61 TYR 0.022 0.002 TYR A 397 PHE 0.040 0.002 PHE A 516 TRP 0.025 0.002 TRP B 28 HIS 0.009 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16823) covalent geometry : angle 0.64421 / 0.33 (22952) hydrogen bonds : bond 0.03753 / 2.56 ( 788) hydrogen bonds : angle 5.31664 / 3.70 ( 2186) metal coordination : bond 0.00313 / 0.19 ( 4) metal coordination : angle 8.17252 / 6.17 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4573.12 seconds wall clock time: 79 minutes 6.35 seconds (4746.35 seconds total)