Starting phenix.real_space_refine on Fri Sep 27 15:40:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8t_44358/09_2024/9b8t_44358.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8t_44358/09_2024/9b8t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8t_44358/09_2024/9b8t_44358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8t_44358/09_2024/9b8t_44358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8t_44358/09_2024/9b8t_44358.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8t_44358/09_2024/9b8t_44358.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 53 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 10221 2.51 5 N 2766 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16399 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9313 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 58, 'TRANS': 1087} Chain breaks: 1 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'SF4': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4940 SG CYS A 663 70.973 79.154 48.069 1.00 72.87 S ATOM 4874 SG CYS A 654 75.834 75.266 45.585 1.00 88.21 S ATOM 5664 SG CYS A 747 69.867 73.512 46.501 1.00 39.67 S ATOM 4858 SG CYS A 651 72.585 74.287 51.633 1.00 72.97 S Time building chain proxies: 9.79, per 1000 atoms: 0.60 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: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A3003 " pdb="FE3 SF4 A3003 " - pdb=" SG CYS A 747 " pdb="FE1 SF4 A3003 " - pdb=" SG CYS A 663 " pdb="FE2 SF4 A3003 " - pdb=" SG CYS A 654 " pdb="FE4 SF4 A3003 " - pdb=" SG CYS A 651 " Number of angles added : 12 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 33.4% alpha, 23.7% beta 22 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.69 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: 8.03 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 6711 1.40 - 1.62: 9942 1.62 - 1.84: 158 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 16823 Sorted by residual: bond pdb=" C PRO A 452 " pdb=" O PRO A 452 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.16e-02 7.43e+03 2.73e+01 bond pdb=" C GLN A 451 " pdb=" O GLN A 451 " ideal model delta sigma weight residual 1.238 1.292 -0.054 1.28e-02 6.10e+03 1.78e+01 bond pdb=" N ASP A 462 " pdb=" CA ASP A 462 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.44e-02 4.82e+03 8.56e+00 bond pdb=" N ILE D 11 " pdb=" CA ILE D 11 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.99e+00 bond pdb=" N ARG A1111 " pdb=" CA ARG A1111 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.52e+00 ... (remaining 16818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 22504 2.92 - 5.84: 374 5.84 - 8.76: 56 8.76 - 11.68: 16 11.68 - 14.60: 2 Bond angle restraints: 22952 Sorted by residual: angle pdb=" CB MET C 244 " pdb=" CG MET C 244 " pdb=" SD MET C 244 " ideal model delta sigma weight residual 112.70 127.30 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CA GLU A 36 " pdb=" CB GLU A 36 " pdb=" CG GLU A 36 " ideal model delta sigma weight residual 114.10 123.78 -9.68 2.00e+00 2.50e-01 2.34e+01 angle pdb=" CA GLU A1173 " pdb=" CB GLU A1173 " pdb=" CG GLU A1173 " ideal model delta sigma weight residual 114.10 123.02 -8.92 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB ARG A 154 " pdb=" CG ARG A 154 " pdb=" CD ARG A 154 " ideal model delta sigma weight residual 111.30 121.51 -10.21 2.30e+00 1.89e-01 1.97e+01 angle pdb=" N VAL A 785 " pdb=" CA VAL A 785 " pdb=" C VAL A 785 " ideal model delta sigma weight residual 108.65 102.25 6.40 1.45e+00 4.76e-01 1.95e+01 ... (remaining 22947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 9302 28.46 - 56.91: 792 56.91 - 85.37: 64 85.37 - 113.83: 3 113.83 - 142.29: 3 Dihedral angle restraints: 10164 sinusoidal: 4501 harmonic: 5663 Sorted by residual: dihedral pdb=" C2 TTP A3001 " pdb=" C1' TTP A3001 " pdb=" N1 TTP A3001 " pdb=" O4' TTP A3001 " ideal model delta sinusoidal sigma weight residual 301.68 159.40 142.29 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" O3A TTP A3001 " pdb=" O3B TTP A3001 " pdb=" PB TTP A3001 " pdb=" PG TTP A3001 " ideal model delta sinusoidal sigma weight residual 179.98 -53.61 -126.41 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" O5' TTP A3001 " pdb=" O3A TTP A3001 " pdb=" PA TTP A3001 " pdb=" PB TTP A3001 " ideal model delta sinusoidal sigma weight residual 180.02 54.81 125.21 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 10161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2201 0.077 - 0.154: 330 0.154 - 0.231: 23 0.231 - 0.308: 2 0.308 - 0.385: 1 Chirality restraints: 2557 Sorted by residual: chirality pdb=" CB VAL A 785 " pdb=" CA VAL A 785 " pdb=" CG1 VAL A 785 " pdb=" CG2 VAL A 785 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CG LEU A 272 " pdb=" CB LEU A 272 " pdb=" CD1 LEU A 272 " pdb=" CD2 LEU A 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CG LEU A 897 " pdb=" CB LEU A 897 " pdb=" CD1 LEU A 897 " pdb=" CD2 LEU A 897 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2554 not shown) Planarity restraints: 2781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 450 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C GLU A 450 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU A 450 " 0.032 2.00e-02 2.50e+03 pdb=" N GLN A 451 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 516 " 0.035 2.00e-02 2.50e+03 3.36e-02 1.98e+01 pdb=" CG PHE A 516 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE A 516 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 516 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 516 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 516 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 516 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " -0.022 2.00e-02 2.50e+03 2.18e-02 9.49e+00 pdb=" CG TYR A 103 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 ... (remaining 2778 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 220 2.65 - 3.21: 13288 3.21 - 3.77: 26847 3.77 - 4.34: 35556 4.34 - 4.90: 57169 Nonbonded interactions: 133080 Sorted by model distance: nonbonded pdb=" O VAL A 627 " pdb="MG MG A3002 " model vdw 2.085 2.170 nonbonded pdb=" O1G TTP A3001 " pdb="MG MG A3002 " model vdw 2.200 2.170 nonbonded pdb=" OH TYR A 754 " pdb=" O PHE A 815 " model vdw 2.278 3.040 nonbonded pdb=" O GLU B 25 " pdb=" OG SER B 39 " model vdw 2.292 3.040 nonbonded pdb=" OG SER D 43 " pdb=" OH TYR D 211 " model vdw 2.299 3.040 ... (remaining 133075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.170 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16823 Z= 0.325 Angle : 0.957 14.604 22952 Z= 0.520 Chirality : 0.054 0.385 2557 Planarity : 0.007 0.066 2781 Dihedral : 18.825 142.286 6494 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.30 % Allowed : 25.52 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 1919 helix: -1.26 (0.19), residues: 571 sheet: -0.39 (0.23), residues: 506 loop : -1.85 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 28 HIS 0.010 0.001 HIS A 350 PHE 0.076 0.003 PHE A 516 TYR 0.054 0.003 TYR A 103 ARG 0.017 0.001 ARG A 728 *********************** 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 fitting. rotamer outliers: 73 poor density : 225 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7348 (tm) cc_final: 0.7123 (mp) REVERT: A 221 MET cc_start: 0.7315 (mpt) cc_final: 0.6725 (ptt) REVERT: A 295 MET cc_start: 0.5927 (mtm) cc_final: 0.5693 (mmt) REVERT: A 715 GLN cc_start: 0.6378 (mt0) cc_final: 0.5876 (mm-40) REVERT: A 1083 LYS cc_start: 0.5645 (mmmt) cc_final: 0.5133 (mttt) REVERT: B 94 ASP cc_start: 0.3752 (m-30) cc_final: 0.3028 (p0) REVERT: B 197 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6447 (pt) REVERT: B 217 LYS cc_start: 0.6445 (mmmm) cc_final: 0.6200 (mmtt) REVERT: B 246 HIS cc_start: 0.6286 (p90) cc_final: 0.6081 (p90) REVERT: C 1 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5196 (ttm) REVERT: C 244 MET cc_start: 0.7148 (tpp) cc_final: 0.6740 (ttm) REVERT: D 179 ASN cc_start: 0.7406 (p0) cc_final: 0.6959 (p0) REVERT: D 244 MET cc_start: 0.4896 (tpp) cc_final: 0.4599 (tpp) outliers start: 73 outliers final: 39 residues processed: 272 average time/residue: 1.0339 time to fit residues: 319.5298 Evaluate side-chains 234 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 8.9990 chunk 148 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 394 GLN A 475 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16823 Z= 0.195 Angle : 0.608 8.843 22952 Z= 0.319 Chirality : 0.043 0.160 2557 Planarity : 0.005 0.046 2781 Dihedral : 15.676 140.389 2732 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.77 % Allowed : 23.16 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 1919 helix: -0.22 (0.20), residues: 577 sheet: -0.22 (0.23), residues: 510 loop : -1.49 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 28 HIS 0.004 0.001 HIS A 229 PHE 0.035 0.002 PHE C 215 TYR 0.014 0.002 TYR A 468 ARG 0.005 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 208 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 THR cc_start: 0.6870 (m) cc_final: 0.6432 (t) REVERT: A 46 LEU cc_start: 0.7364 (tm) cc_final: 0.7087 (mp) REVERT: A 151 ASN cc_start: 0.5263 (p0) cc_final: 0.4622 (m-40) REVERT: A 715 GLN cc_start: 0.6295 (mt0) cc_final: 0.5832 (mm-40) REVERT: A 921 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.5111 (m-80) REVERT: A 1083 LYS cc_start: 0.5442 (mmmt) cc_final: 0.5038 (mttt) REVERT: A 1189 LEU cc_start: 0.7710 (mp) cc_final: 0.7438 (pp) REVERT: B 94 ASP cc_start: 0.3840 (m-30) cc_final: 0.3139 (p0) REVERT: B 197 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6613 (pt) REVERT: C 1 MET cc_start: 0.6046 (mmt) cc_final: 0.5105 (ttm) REVERT: D 132 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: D 138 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7139 (tmtt) REVERT: D 179 ASN cc_start: 0.7097 (p0) cc_final: 0.6873 (p0) outliers start: 98 outliers final: 35 residues processed: 279 average time/residue: 0.9912 time to fit residues: 317.3988 Evaluate side-chains 228 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 988 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 138 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 chunk 192 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 177 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS A1180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16823 Z= 0.281 Angle : 0.656 8.967 22952 Z= 0.341 Chirality : 0.044 0.173 2557 Planarity : 0.005 0.038 2781 Dihedral : 15.621 134.520 2686 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.48 % Allowed : 23.28 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.18), residues: 1919 helix: -0.11 (0.21), residues: 593 sheet: -0.12 (0.23), residues: 510 loop : -1.48 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 40 HIS 0.013 0.001 HIS A 229 PHE 0.023 0.002 PHE C 215 TYR 0.025 0.002 TYR A 631 ARG 0.008 0.001 ARG A 37 *********************** 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 328 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 218 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5919 (mmm160) cc_final: 0.5010 (mmp80) REVERT: A 151 ASN cc_start: 0.5211 (p0) cc_final: 0.4501 (m-40) REVERT: A 278 THR cc_start: 0.5574 (OUTLIER) cc_final: 0.5348 (t) REVERT: A 299 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6485 (mtm) REVERT: A 715 GLN cc_start: 0.6375 (mt0) cc_final: 0.5924 (mm-40) REVERT: A 821 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.4990 (ptm160) REVERT: A 878 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: A 921 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.5339 (m-80) REVERT: A 951 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6768 (mtmm) REVERT: A 972 GLU cc_start: 0.6920 (mp0) cc_final: 0.6536 (mt-10) REVERT: A 1083 LYS cc_start: 0.5631 (mmmt) cc_final: 0.5151 (mttt) REVERT: A 1189 LEU cc_start: 0.7951 (mp) cc_final: 0.7700 (pp) REVERT: B 94 ASP cc_start: 0.3816 (m-30) cc_final: 0.3175 (OUTLIER) REVERT: B 204 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6925 (pp30) REVERT: C 1 MET cc_start: 0.6044 (mmt) cc_final: 0.5254 (ttm) REVERT: C 41 ASP cc_start: 0.5807 (t0) cc_final: 0.5292 (t0) REVERT: C 159 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7203 (m) REVERT: D 138 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7450 (tmtt) REVERT: D 179 ASN cc_start: 0.7235 (p0) cc_final: 0.7023 (p0) outliers start: 110 outliers final: 50 residues processed: 300 average time/residue: 0.9242 time to fit residues: 318.0178 Evaluate side-chains 252 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 194 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 988 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 209 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 176 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 119 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 0.0030 chunk 93 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16823 Z= 0.181 Angle : 0.587 8.856 22952 Z= 0.305 Chirality : 0.042 0.159 2557 Planarity : 0.004 0.040 2781 Dihedral : 15.397 139.453 2683 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.30 % Allowed : 24.57 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.18), residues: 1919 helix: 0.18 (0.21), residues: 596 sheet: -0.02 (0.23), residues: 506 loop : -1.48 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 28 HIS 0.010 0.001 HIS A 229 PHE 0.045 0.002 PHE C 215 TYR 0.018 0.002 TYR C 249 ARG 0.005 0.000 ARG A 37 *********************** 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 fitting. rotamer outliers: 90 poor density : 208 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5999 (mmm160) cc_final: 0.5186 (mmp80) REVERT: A 46 LEU cc_start: 0.7156 (tm) cc_final: 0.6845 (mp) REVERT: A 151 ASN cc_start: 0.5251 (p0) cc_final: 0.4663 (m-40) REVERT: A 446 ARG cc_start: 0.1916 (OUTLIER) cc_final: 0.1570 (mmp-170) REVERT: A 715 GLN cc_start: 0.6265 (mt0) cc_final: 0.5875 (mm-40) REVERT: A 878 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: A 1030 PHE cc_start: 0.6353 (t80) cc_final: 0.6025 (t80) REVERT: A 1083 LYS cc_start: 0.5553 (mmmt) cc_final: 0.5118 (mttt) REVERT: B 47 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7018 (tp) REVERT: B 94 ASP cc_start: 0.3579 (m-30) cc_final: 0.3163 (p0) REVERT: B 199 MET cc_start: 0.4253 (ttm) cc_final: 0.3950 (ptm) REVERT: B 204 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6700 (pp30) REVERT: C 1 MET cc_start: 0.6108 (mmt) cc_final: 0.5908 (mmm) REVERT: C 41 ASP cc_start: 0.5709 (t0) cc_final: 0.5280 (t0) REVERT: C 159 VAL cc_start: 0.7404 (OUTLIER) cc_final: 0.7199 (m) REVERT: D 59 THR cc_start: 0.7357 (OUTLIER) cc_final: 0.6700 (p) REVERT: D 179 ASN cc_start: 0.7005 (p0) cc_final: 0.6731 (p0) outliers start: 90 outliers final: 44 residues processed: 268 average time/residue: 1.0729 time to fit residues: 328.6433 Evaluate side-chains 238 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 188 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 446 ARG Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 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 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 ILE 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 47 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 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 59 THR Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 96 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16823 Z= 0.205 Angle : 0.605 8.617 22952 Z= 0.311 Chirality : 0.043 0.186 2557 Planarity : 0.004 0.038 2781 Dihedral : 15.352 137.655 2680 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.13 % Allowed : 25.57 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1919 helix: 0.32 (0.21), residues: 594 sheet: 0.04 (0.23), residues: 515 loop : -1.43 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 28 HIS 0.011 0.001 HIS A 229 PHE 0.040 0.002 PHE C 215 TYR 0.017 0.002 TYR D 250 ARG 0.005 0.000 ARG B 149 *********************** 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 283 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 196 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.5265 (OUTLIER) cc_final: 0.4738 (m-40) REVERT: A 299 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6343 (mtm) REVERT: A 446 ARG cc_start: 0.2178 (OUTLIER) cc_final: 0.1455 (mmp-170) REVERT: A 715 GLN cc_start: 0.6319 (mt0) cc_final: 0.5945 (mm-40) REVERT: A 878 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: A 1189 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7218 (pp) REVERT: B 47 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6992 (tp) REVERT: B 116 MET cc_start: 0.5194 (OUTLIER) cc_final: 0.4739 (ptm) REVERT: B 199 MET cc_start: 0.4200 (OUTLIER) cc_final: 0.3988 (ptm) REVERT: B 204 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6787 (pp30) REVERT: C 41 ASP cc_start: 0.5795 (t0) cc_final: 0.5266 (t0) REVERT: C 159 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7266 (m) REVERT: D 1 MET cc_start: 0.2633 (OUTLIER) cc_final: 0.2122 (mtm) REVERT: D 138 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7333 (tmtt) outliers start: 87 outliers final: 42 residues processed: 254 average time/residue: 1.0140 time to fit residues: 293.8240 Evaluate side-chains 242 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG 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 571 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 189 ASP 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 16 LEU 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 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 Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN B 8 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16823 Z= 0.332 Angle : 0.691 8.520 22952 Z= 0.354 Chirality : 0.046 0.174 2557 Planarity : 0.005 0.039 2781 Dihedral : 15.610 134.951 2675 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.19 % Allowed : 25.16 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 1919 helix: -0.06 (0.21), residues: 601 sheet: 0.00 (0.23), residues: 509 loop : -1.45 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 40 HIS 0.011 0.001 HIS A 229 PHE 0.029 0.002 PHE C 215 TYR 0.022 0.002 TYR A 631 ARG 0.004 0.001 ARG B 149 *********************** 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 318 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 213 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5998 (mmp80) cc_final: 0.5348 (mmp80) REVERT: A 151 ASN cc_start: 0.5270 (OUTLIER) cc_final: 0.4616 (m-40) REVERT: A 396 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.5954 (mt-10) REVERT: A 446 ARG cc_start: 0.2071 (OUTLIER) cc_final: 0.1544 (mmp-170) REVERT: A 468 TYR cc_start: 0.6385 (m-80) cc_final: 0.6080 (m-80) REVERT: A 972 GLU cc_start: 0.6970 (mp0) cc_final: 0.6699 (mt-10) REVERT: B 28 TRP cc_start: 0.5038 (m100) cc_final: 0.4556 (m100) REVERT: B 204 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6889 (pp30) REVERT: C 1 MET cc_start: 0.5696 (mmm) cc_final: 0.5116 (mmt) REVERT: C 41 ASP cc_start: 0.6069 (t0) cc_final: 0.5520 (t0) REVERT: C 159 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7396 (m) REVERT: D 138 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7439 (tmtt) outliers start: 105 outliers final: 57 residues processed: 288 average time/residue: 1.0192 time to fit residues: 334.8961 Evaluate side-chains 258 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 195 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 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 991 GLU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 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 45 VAL 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 159 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16823 Z= 0.209 Angle : 0.637 10.672 22952 Z= 0.322 Chirality : 0.043 0.180 2557 Planarity : 0.004 0.036 2781 Dihedral : 15.404 139.063 2675 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.83 % Allowed : 27.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1919 helix: 0.10 (0.21), residues: 602 sheet: 0.06 (0.23), residues: 508 loop : -1.39 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 40 HIS 0.010 0.001 HIS A 229 PHE 0.037 0.002 PHE C 215 TYR 0.018 0.002 TYR A 631 ARG 0.006 0.000 ARG B 149 *********************** 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 286 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 204 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6052 (mmp80) cc_final: 0.5643 (mmp80) REVERT: A 151 ASN cc_start: 0.5296 (OUTLIER) cc_final: 0.4812 (m-40) REVERT: A 281 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5820 (mm) REVERT: A 295 MET cc_start: 0.6132 (mtm) cc_final: 0.5917 (ttm) REVERT: A 299 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6299 (mtm) REVERT: A 396 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5857 (mp0) REVERT: A 444 MET cc_start: 0.0705 (mmm) cc_final: 0.0280 (mtt) REVERT: A 446 ARG cc_start: 0.2222 (OUTLIER) cc_final: 0.1496 (mmp-170) REVERT: A 468 TYR cc_start: 0.6360 (m-80) cc_final: 0.6147 (m-80) REVERT: A 878 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: A 1030 PHE cc_start: 0.6182 (t80) cc_final: 0.5883 (t80) REVERT: B 28 TRP cc_start: 0.5030 (m100) cc_final: 0.4545 (m100) REVERT: B 204 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6884 (pp30) REVERT: C 126 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5894 (pp) REVERT: C 146 ARG cc_start: 0.6246 (mmm160) cc_final: 0.5817 (tpt-90) REVERT: C 147 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5917 (mp) REVERT: D 20 LYS cc_start: 0.7102 (tmtt) cc_final: 0.6845 (tttm) REVERT: D 138 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7402 (tmtt) REVERT: D 184 GLN cc_start: 0.5591 (mp-120) cc_final: 0.5352 (mp10) outliers start: 82 outliers final: 39 residues processed: 259 average time/residue: 1.0676 time to fit residues: 316.3209 Evaluate side-chains 238 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 CYS 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 258 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 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 989 VAL Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 119 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 7 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 HIS 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 138 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.0470 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 148 optimal weight: 7.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16823 Z= 0.198 Angle : 0.632 12.077 22952 Z= 0.318 Chirality : 0.042 0.174 2557 Planarity : 0.004 0.039 2781 Dihedral : 15.311 138.387 2673 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.59 % Allowed : 28.76 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1919 helix: 0.18 (0.21), residues: 609 sheet: 0.12 (0.23), residues: 506 loop : -1.36 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 40 HIS 0.009 0.001 HIS A 229 PHE 0.029 0.002 PHE D 2 TYR 0.015 0.002 TYR A 397 ARG 0.007 0.000 ARG B 149 *********************** 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 278 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 217 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5909 (mmp80) cc_final: 0.5580 (mmp80) REVERT: A 151 ASN cc_start: 0.5364 (OUTLIER) cc_final: 0.4923 (m-40) REVERT: A 276 ILE cc_start: 0.6293 (pp) cc_final: 0.5879 (pp) REVERT: A 281 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5791 (mm) REVERT: A 295 MET cc_start: 0.5944 (mtm) cc_final: 0.5690 (ttm) REVERT: A 299 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6330 (mtm) REVERT: A 396 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: A 444 MET cc_start: 0.0578 (mmm) cc_final: 0.0297 (mtt) REVERT: A 446 ARG cc_start: 0.2114 (OUTLIER) cc_final: 0.1794 (mmp-170) REVERT: A 468 TYR cc_start: 0.6374 (m-80) cc_final: 0.6167 (m-80) REVERT: A 878 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.7071 (m-10) REVERT: A 1030 PHE cc_start: 0.6091 (t80) cc_final: 0.5810 (t80) REVERT: B 47 LEU cc_start: 0.7345 (tm) cc_final: 0.7115 (tp) REVERT: B 64 ARG cc_start: 0.6193 (ptt90) cc_final: 0.5861 (ptt-90) REVERT: B 199 MET cc_start: 0.5342 (tmm) cc_final: 0.5127 (ptm) REVERT: B 204 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6888 (pp30) REVERT: C 1 MET cc_start: 0.5822 (mmm) cc_final: 0.5026 (ttt) REVERT: C 41 ASP cc_start: 0.6119 (t0) cc_final: 0.5267 (t0) REVERT: C 126 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5993 (pp) REVERT: C 139 MET cc_start: 0.5194 (tmt) cc_final: 0.4859 (tmt) REVERT: C 146 ARG cc_start: 0.6139 (mmm160) cc_final: 0.5850 (tpt-90) REVERT: D 20 LYS cc_start: 0.7114 (tmtt) cc_final: 0.6881 (tttm) REVERT: D 53 ARG cc_start: 0.5234 (ptp-170) cc_final: 0.4505 (mmp-170) REVERT: D 211 TYR cc_start: 0.7789 (m-80) cc_final: 0.7587 (m-80) outliers start: 61 outliers final: 37 residues processed: 259 average time/residue: 1.0981 time to fit residues: 322.1318 Evaluate side-chains 245 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 170 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 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 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 119 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 7 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 184 GLN D 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16823 Z= 0.298 Angle : 0.716 12.065 22952 Z= 0.360 Chirality : 0.045 0.236 2557 Planarity : 0.004 0.038 2781 Dihedral : 15.525 135.888 2672 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.60 % Allowed : 28.46 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1919 helix: 0.09 (0.21), residues: 598 sheet: -0.01 (0.23), residues: 509 loop : -1.43 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 40 HIS 0.009 0.001 HIS A 229 PHE 0.061 0.002 PHE A 516 TYR 0.025 0.002 TYR A 631 ARG 0.008 0.001 ARG A 346 *********************** 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 283 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 205 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.5303 (OUTLIER) cc_final: 0.4791 (m-40) REVERT: A 276 ILE cc_start: 0.6191 (pp) cc_final: 0.5847 (pp) REVERT: A 299 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6442 (mtm) REVERT: A 396 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5878 (mt-10) REVERT: A 444 MET cc_start: 0.0899 (mmm) cc_final: 0.0435 (mtt) REVERT: A 446 ARG cc_start: 0.2382 (OUTLIER) cc_final: 0.1538 (mmp-170) REVERT: A 468 TYR cc_start: 0.6424 (m-80) cc_final: 0.6144 (m-80) REVERT: A 599 VAL cc_start: 0.5642 (OUTLIER) cc_final: 0.5438 (p) REVERT: A 878 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6852 (m-10) REVERT: A 972 GLU cc_start: 0.6908 (mp0) cc_final: 0.6673 (mt-10) REVERT: A 1094 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5651 (mp) REVERT: B 64 ARG cc_start: 0.6274 (ptt90) cc_final: 0.5911 (ptt-90) REVERT: B 72 LEU cc_start: 0.8080 (tp) cc_final: 0.7734 (tp) REVERT: B 199 MET cc_start: 0.5210 (tmm) cc_final: 0.4947 (ptm) REVERT: B 204 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6946 (pp30) REVERT: C 1 MET cc_start: 0.5821 (mmm) cc_final: 0.5036 (ttt) REVERT: C 41 ASP cc_start: 0.6203 (t0) cc_final: 0.5359 (t0) REVERT: C 66 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6564 (tp) REVERT: C 126 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6071 (pp) REVERT: C 146 ARG cc_start: 0.6223 (mmm160) cc_final: 0.5853 (tpt-90) REVERT: C 147 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5925 (mp) REVERT: D 20 LYS cc_start: 0.7246 (tmtt) cc_final: 0.7031 (tttm) REVERT: D 199 MET cc_start: 0.6100 (mpp) cc_final: 0.5887 (mtt) outliers start: 78 outliers final: 51 residues processed: 261 average time/residue: 1.0655 time to fit residues: 316.5171 Evaluate side-chains 254 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 192 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 151 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 PHE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 189 ASP 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 7 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16823 Z= 0.210 Angle : 0.664 10.971 22952 Z= 0.335 Chirality : 0.043 0.248 2557 Planarity : 0.004 0.039 2781 Dihedral : 15.364 139.464 2672 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.12 % Allowed : 30.35 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1919 helix: 0.19 (0.21), residues: 603 sheet: 0.01 (0.23), residues: 507 loop : -1.44 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 40 HIS 0.009 0.001 HIS A 229 PHE 0.041 0.002 PHE A 516 TYR 0.027 0.002 TYR A 397 ARG 0.020 0.001 ARG D 61 ********************** 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 252 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.5376 (p0) cc_final: 0.4999 (m-40) REVERT: A 276 ILE cc_start: 0.6143 (pp) cc_final: 0.5852 (pp) REVERT: A 295 MET cc_start: 0.6270 (mtm) cc_final: 0.5968 (ttm) REVERT: A 396 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5953 (mt-10) REVERT: A 444 MET cc_start: 0.0741 (mmm) cc_final: 0.0393 (mtt) REVERT: A 446 ARG cc_start: 0.2124 (OUTLIER) cc_final: 0.1734 (mmp-170) REVERT: B 47 LEU cc_start: 0.7227 (tm) cc_final: 0.7025 (tp) REVERT: B 64 ARG cc_start: 0.6264 (ptt90) cc_final: 0.5921 (ptt-90) REVERT: B 204 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6884 (pp30) REVERT: C 1 MET cc_start: 0.5818 (mmm) cc_final: 0.5069 (ttt) REVERT: C 41 ASP cc_start: 0.6219 (t0) cc_final: 0.5399 (t0) REVERT: C 66 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6653 (tp) REVERT: C 126 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6099 (pp) REVERT: C 143 GLU cc_start: 0.5127 (pm20) cc_final: 0.4825 (pm20) REVERT: C 146 ARG cc_start: 0.6130 (mmm160) cc_final: 0.5818 (tpt-90) REVERT: C 147 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5742 (mp) REVERT: D 20 LYS cc_start: 0.7124 (tmtt) cc_final: 0.6910 (tttm) outliers start: 53 outliers final: 40 residues processed: 242 average time/residue: 1.0409 time to fit residues: 289.3366 Evaluate side-chains 237 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 549 SER 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 574 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 119 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 7 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.227852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.198369 restraints weight = 19412.170| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 2.91 r_work: 0.4182 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16823 Z= 0.282 Angle : 0.704 11.590 22952 Z= 0.354 Chirality : 0.045 0.184 2557 Planarity : 0.004 0.066 2781 Dihedral : 15.504 135.827 2672 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.89 % Allowed : 29.88 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1919 helix: 0.15 (0.21), residues: 596 sheet: -0.06 (0.23), residues: 510 loop : -1.48 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 40 HIS 0.009 0.001 HIS A 229 PHE 0.047 0.002 PHE A 516 TYR 0.037 0.002 TYR A 397 ARG 0.019 0.001 ARG A 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5574.57 seconds wall clock time: 99 minutes 8.30 seconds (5948.30 seconds total)