Starting phenix.real_space_refine on Fri Jul 3 03:04:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oh6_12895/07_2026/7oh6_12895.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7470 2.51 5 N 1858 2.21 5 O 2167 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11552 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2842 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 123 Unusual residues: {' MG': 1, '2Y5': 1, 'ALF': 1, 'Q3G': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.62, per 1000 atoms: 0.23 Number of scatterers: 11552 At special positions: 0 Unit cell: (73.2152, 106.214, 174.273, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2167 8.00 N 1858 7.00 C 7470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.14 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=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 501 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 487.7 milliseconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 11 sheets defined 46.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 213 through 222 removed outlier: 4.125A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 239 through 243 removed outlier: 4.015A pdb=" N VAL A 242 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 243 " --> pdb=" O PRO A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 243' Processing helix chain 'A' and resid 248 through 281 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.675A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.848A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.588A pdb=" N LEU A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 481 " --> pdb=" O SER A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 487 through 503 removed outlier: 4.202A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 508 through 526 removed outlier: 4.178A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 530 removed outlier: 6.757A pdb=" N ASP A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 530' Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.676A pdb=" N LEU A 547 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.968A pdb=" N ASP A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.507A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 765 through 782 removed outlier: 3.655A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 795 removed outlier: 3.846A pdb=" N GLU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.645A pdb=" N ALA A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 883 removed outlier: 3.554A pdb=" N GLU A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 899 through 906 removed outlier: 4.071A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 932 through 944 removed outlier: 3.948A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 965 Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 992 through 1014 removed outlier: 3.546A pdb=" N LEU A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A1005 " --> pdb=" O GLY A1001 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A1009 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1042 through 1053 removed outlier: 4.505A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A1053 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 removed outlier: 3.712A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1076 Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1085 Processing helix chain 'A' and resid 1090 through 1116 Processing helix chain 'A' and resid 1131 through 1154 removed outlier: 4.078A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1180 removed outlier: 3.709A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1194 through 1201 Processing helix chain 'A' and resid 1202 through 1231 removed outlier: 4.075A pdb=" N TRP A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 5.055A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A1231 " --> pdb=" O LYS A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 3.536A pdb=" N TYR A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 69 removed outlier: 3.852A pdb=" N LEU C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix removed outlier: 3.783A pdb=" N THR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.370A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 180 removed outlier: 3.811A pdb=" N CYS C 176 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.499A pdb=" N ALA C 194 " --> pdb=" O CYS C 190 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.926A pdb=" N MET C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.688A pdb=" N LEU C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 357 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 288 Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.515A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.881A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 532 through 533 removed outlier: 3.960A pdb=" N TYR A 533 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.368A pdb=" N GLY A 968 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A 987 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY A 970 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE A 831 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N CYS A 926 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 833 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 893 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ILE A 925 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N CYS A 927 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 897 " --> pdb=" O CYS A 927 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 577 removed outlier: 5.441A pdb=" N ILE A 569 " --> pdb=" O LYS A 812 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 812 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 706 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE A 695 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A 708 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.383A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.497A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.344A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 494 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1862 1.31 - 1.44: 3208 1.44 - 1.56: 6655 1.56 - 1.69: 5 1.69 - 1.82: 81 Bond restraints: 11811 Sorted by residual: bond pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.806 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.791 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" F4 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.686 1.790 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.684 1.778 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C18 Q3G A1504 " pdb=" O20 Q3G A1504 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 11806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.98: 15995 13.98 - 27.97: 4 27.97 - 41.95: 0 41.95 - 55.93: 0 55.93 - 69.91: 2 Bond angle restraints: 16001 Sorted by residual: angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.54 -69.91 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 177.97 -69.29 3.00e+00 1.11e-01 5.34e+02 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 110.21 89.89 20.32 3.00e+00 1.11e-01 4.59e+01 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.02 89.28 19.74 3.00e+00 1.11e-01 4.33e+01 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.69 90.35 19.34 3.00e+00 1.11e-01 4.15e+01 ... (remaining 15996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.28: 6802 25.28 - 50.57: 203 50.57 - 75.85: 27 75.85 - 101.14: 10 101.14 - 126.42: 6 Dihedral angle restraints: 7048 sinusoidal: 2898 harmonic: 4150 Sorted by residual: dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" C33 2Y5 A1501 " pdb=" C34 2Y5 A1501 " pdb=" C35 2Y5 A1501 " pdb=" C36 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 56.12 -177.46 -126.42 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C11 Q3G A1504 " pdb=" C12 Q3G A1504 " pdb=" C13 Q3G A1504 " pdb=" C14 Q3G A1504 " ideal model delta sinusoidal sigma weight residual 179.08 -56.22 -124.70 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 7045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.994: 1821 0.994 - 1.988: 0 1.988 - 2.981: 0 2.981 - 3.975: 0 3.975 - 4.969: 1 Chirality restraints: 1822 Sorted by residual: chirality pdb=" C1 2Y5 A1501 " pdb=" C2 2Y5 A1501 " pdb=" C6 2Y5 A1501 " pdb=" O1 2Y5 A1501 " both_signs ideal model delta sigma weight residual False -2.53 2.43 -4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 2Y5 A1501 " pdb=" C4 2Y5 A1501 " pdb=" C6 2Y5 A1501 " pdb=" O5 2Y5 A1501 " both_signs ideal model delta sigma weight residual False 2.29 2.49 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1819 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 746 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU A 746 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU A 746 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 747 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 621 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PRO A 621 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 621 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 622 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 745 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C HIS A 745 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS A 745 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 746 " 0.018 2.00e-02 2.50e+03 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 26 2.36 - 2.99: 6042 2.99 - 3.63: 16204 3.63 - 4.26: 25733 4.26 - 4.90: 43704 Nonbonded interactions: 91709 Sorted by model distance: nonbonded pdb=" F4 ALF A1502 " pdb="MG MG A1503 " model vdw 1.720 2.120 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 1.974 2.170 nonbonded pdb=" OD2 ASP A 560 " pdb="MG MG A1503 " model vdw 1.978 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1602 " model vdw 2.007 2.170 nonbonded pdb=" OD1 ASP A 954 " pdb="MG MG A1503 " model vdw 2.085 2.170 ... (remaining 91704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.007 0.589 11820 Z= 0.576 Angle : 1.082 69.913 16023 Z= 0.439 Chirality : 0.124 4.969 1822 Planarity : 0.005 0.060 1996 Dihedral : 12.924 126.423 4366 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.20 % Allowed : 4.39 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.21), residues: 1410 helix: -1.20 (0.20), residues: 587 sheet: -1.40 (0.34), residues: 202 loop : -2.10 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.012 0.001 TYR C 141 PHE 0.010 0.001 PHE C 317 TRP 0.008 0.001 TRP A1132 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (11811) covalent geometry : angle 1.08181 / 0.44 (16001) SS BOND : bond 0.08064 / 5.73 ( 2) SS BOND : angle 1.20983 / 0.78 ( 4) hydrogen bonds : bond 0.13762 / 8.23 ( 494) hydrogen bonds : angle 6.10312 / 4.34 ( 1398) Misc. bond : bond 0.58888 / 39.26 ( 1) link_BETA1-4 : bond 0.00489 / 0.33 ( 3) link_BETA1-4 : angle 1.33005 / 0.89 ( 9) link_NAG-ASN : bond 0.00334 / 0.21 ( 3) link_NAG-ASN : angle 1.00633 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8198 (tttt) cc_final: 0.7991 (mmpt) REVERT: A 277 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5872 (mmmt) REVERT: A 296 GLU cc_start: 0.7178 (tt0) cc_final: 0.6906 (tm-30) REVERT: A 437 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7733 (mtm180) REVERT: A 560 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6613 (p0) REVERT: A 637 ILE cc_start: 0.7819 (mt) cc_final: 0.7595 (mt) REVERT: A 866 ARG cc_start: 0.7197 (tmt170) cc_final: 0.6919 (tpt170) REVERT: A 1219 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.5667 (tpt90) REVERT: C 165 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7371 (mm-30) REVERT: C 168 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6728 (mmtt) outliers start: 15 outliers final: 4 residues processed: 210 average time/residue: 0.5122 time to fit residues: 116.4520 Evaluate side-chains 113 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1219 ARG Chi-restraints excluded: chain C residue 176 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 376 ASN A 409 ASN A 580 HIS A 966 HIS A1242 GLN C 237 ASN C 305 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.106831 restraints weight = 16033.771| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.66 r_work: 0.3487 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11820 Z= 0.135 Angle : 0.798 30.648 16023 Z= 0.351 Chirality : 0.043 0.236 1822 Planarity : 0.005 0.047 1996 Dihedral : 10.739 121.344 1670 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 2.39 % Allowed : 10.77 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1410 helix: -0.24 (0.21), residues: 601 sheet: -0.99 (0.35), residues: 205 loop : -1.80 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 744 TYR 0.020 0.002 TYR C 77 PHE 0.012 0.001 PHE A 495 TRP 0.011 0.001 TRP C 266 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11811) covalent geometry : angle 0.79683 / 0.35 (16001) SS BOND : bond 0.00562 / 0.40 ( 2) SS BOND : angle 1.16846 / 0.70 ( 4) hydrogen bonds : bond 0.04101 / 2.68 ( 494) hydrogen bonds : angle 4.70472 / 3.32 ( 1398) Misc. bond : bond 0.00078 / 0.05 ( 1) link_BETA1-4 : bond 0.00458 / 0.30 ( 3) link_BETA1-4 : angle 1.46992 / 0.98 ( 9) link_NAG-ASN : bond 0.00402 / 0.25 ( 3) link_NAG-ASN : angle 0.99795 / 0.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8167 (tttt) cc_final: 0.7823 (mmpt) REVERT: A 277 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5878 (mmmt) REVERT: A 296 GLU cc_start: 0.7428 (tt0) cc_final: 0.6941 (tm-30) REVERT: A 336 THR cc_start: 0.7640 (p) cc_final: 0.7256 (t) REVERT: A 386 MET cc_start: 0.6645 (ttp) cc_final: 0.6380 (ttm) REVERT: A 437 ARG cc_start: 0.8398 (mtt90) cc_final: 0.7828 (mtm180) REVERT: A 560 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7283 (p0) REVERT: A 675 ASN cc_start: 0.7836 (m-40) cc_final: 0.7595 (m-40) REVERT: A 690 TYR cc_start: 0.5937 (m-80) cc_final: 0.5561 (m-80) REVERT: A 691 GLN cc_start: 0.6806 (mm110) cc_final: 0.6135 (tm-30) REVERT: A 761 MET cc_start: 0.6059 (tmm) cc_final: 0.5807 (tmm) REVERT: C 143 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8765 (mm) REVERT: C 165 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7635 (mm-30) outliers start: 30 outliers final: 14 residues processed: 135 average time/residue: 0.5197 time to fit residues: 76.2334 Evaluate side-chains 115 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.152735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107448 restraints weight = 16069.229| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.70 r_work: 0.3501 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11820 Z= 0.112 Angle : 0.766 29.638 16023 Z= 0.332 Chirality : 0.042 0.218 1822 Planarity : 0.004 0.046 1996 Dihedral : 9.822 115.630 1664 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 2.55 % Allowed : 11.81 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1410 helix: 0.41 (0.22), residues: 590 sheet: -0.66 (0.35), residues: 198 loop : -1.52 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 850 TYR 0.019 0.001 TYR A 738 PHE 0.013 0.001 PHE A 491 TRP 0.012 0.001 TRP A1172 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11811) covalent geometry : angle 0.76523 / 0.33 (16001) SS BOND : bond 0.00481 / 0.34 ( 2) SS BOND : angle 1.35437 / 0.79 ( 4) hydrogen bonds : bond 0.03491 / 2.31 ( 494) hydrogen bonds : angle 4.38593 / 3.08 ( 1398) Misc. bond : bond 0.00146 / 0.10 ( 1) link_BETA1-4 : bond 0.00437 / 0.28 ( 3) link_BETA1-4 : angle 1.41998 / 0.94 ( 9) link_NAG-ASN : bond 0.00354 / 0.22 ( 3) link_NAG-ASN : angle 1.00072 / 0.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8161 (tttt) cc_final: 0.7831 (mmpt) REVERT: A 277 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5831 (mmmt) REVERT: A 296 GLU cc_start: 0.7464 (tt0) cc_final: 0.6913 (tm-30) REVERT: A 336 THR cc_start: 0.7700 (p) cc_final: 0.7289 (t) REVERT: A 386 MET cc_start: 0.6636 (ttp) cc_final: 0.6423 (ttm) REVERT: A 400 MET cc_start: 0.8629 (ttt) cc_final: 0.8392 (ttt) REVERT: A 435 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 437 ARG cc_start: 0.8460 (mtt90) cc_final: 0.7873 (mtm180) REVERT: A 560 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7174 (p0) REVERT: A 675 ASN cc_start: 0.7630 (m-40) cc_final: 0.7233 (m-40) REVERT: A 690 TYR cc_start: 0.5992 (m-80) cc_final: 0.5615 (m-80) REVERT: A 691 GLN cc_start: 0.6711 (mm110) cc_final: 0.5971 (tm-30) REVERT: A 698 PHE cc_start: 0.6323 (t80) cc_final: 0.5944 (t80) REVERT: A 705 MET cc_start: 0.6201 (tpp) cc_final: 0.5714 (ttm) REVERT: A 761 MET cc_start: 0.6308 (tmm) cc_final: 0.6009 (tmm) REVERT: A 815 ASP cc_start: 0.8426 (t0) cc_final: 0.8206 (t0) REVERT: A 1228 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7688 (tmt170) REVERT: C 165 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7653 (mm-30) outliers start: 32 outliers final: 16 residues processed: 125 average time/residue: 0.4362 time to fit residues: 60.3983 Evaluate side-chains 115 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.148999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104724 restraints weight = 15989.227| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.61 r_work: 0.3467 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11820 Z= 0.153 Angle : 0.785 29.883 16023 Z= 0.342 Chirality : 0.044 0.219 1822 Planarity : 0.004 0.047 1996 Dihedral : 9.548 111.582 1663 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 3.43 % Allowed : 12.93 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.23), residues: 1410 helix: 0.56 (0.22), residues: 590 sheet: -0.77 (0.34), residues: 205 loop : -1.46 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 710 TYR 0.021 0.002 TYR A 738 PHE 0.022 0.002 PHE A 709 TRP 0.013 0.001 TRP A1172 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (11811) covalent geometry : angle 0.78404 / 0.34 (16001) SS BOND : bond 0.00267 / 0.19 ( 2) SS BOND : angle 1.52924 / 1.14 ( 4) hydrogen bonds : bond 0.03796 / 2.49 ( 494) hydrogen bonds : angle 4.31224 / 3.04 ( 1398) Misc. bond : bond 0.00068 / 0.05 ( 1) link_BETA1-4 : bond 0.00411 / 0.27 ( 3) link_BETA1-4 : angle 1.44107 / 1.00 ( 9) link_NAG-ASN : bond 0.00374 / 0.22 ( 3) link_NAG-ASN : angle 1.06560 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8222 (tttt) cc_final: 0.7867 (mmpt) REVERT: A 277 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5882 (mmmt) REVERT: A 296 GLU cc_start: 0.7423 (tt0) cc_final: 0.6904 (tm-30) REVERT: A 336 THR cc_start: 0.7872 (p) cc_final: 0.7521 (t) REVERT: A 386 MET cc_start: 0.6856 (ttp) cc_final: 0.6590 (ttm) REVERT: A 400 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8377 (ttt) REVERT: A 435 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8157 (pp) REVERT: A 437 ARG cc_start: 0.8452 (mtt90) cc_final: 0.7890 (mtm180) REVERT: A 698 PHE cc_start: 0.6256 (t80) cc_final: 0.5991 (t80) REVERT: A 705 MET cc_start: 0.6283 (tpp) cc_final: 0.5936 (ttm) REVERT: A 761 MET cc_start: 0.6485 (tmm) cc_final: 0.6197 (tmm) REVERT: A 815 ASP cc_start: 0.8438 (t0) cc_final: 0.8215 (t0) REVERT: C 165 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7678 (mm-30) outliers start: 43 outliers final: 21 residues processed: 121 average time/residue: 0.4009 time to fit residues: 54.6740 Evaluate side-chains 114 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1242 GLN C 110 GLN C 364 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.148018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103072 restraints weight = 16354.650| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.66 r_work: 0.3433 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11820 Z= 0.184 Angle : 0.811 30.015 16023 Z= 0.357 Chirality : 0.045 0.214 1822 Planarity : 0.004 0.049 1996 Dihedral : 9.611 110.426 1663 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 3.43 % Allowed : 14.37 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.22), residues: 1410 helix: 0.57 (0.22), residues: 589 sheet: -0.76 (0.35), residues: 203 loop : -1.53 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 710 TYR 0.016 0.002 TYR A 738 PHE 0.023 0.002 PHE A 709 TRP 0.016 0.001 TRP A1172 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (11811) covalent geometry : angle 0.80930 / 0.36 (16001) SS BOND : bond 0.00471 / 0.34 ( 2) SS BOND : angle 1.77338 / 1.40 ( 4) hydrogen bonds : bond 0.04129 / 2.70 ( 494) hydrogen bonds : angle 4.32893 / 3.06 ( 1398) Misc. bond : bond 0.00033 / 0.02 ( 1) link_BETA1-4 : bond 0.00461 / 0.30 ( 3) link_BETA1-4 : angle 1.52009 / 1.04 ( 9) link_NAG-ASN : bond 0.00379 / 0.22 ( 3) link_NAG-ASN : angle 1.24301 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8188 (tttt) cc_final: 0.7811 (mmpt) REVERT: A 277 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5990 (mmmt) REVERT: A 336 THR cc_start: 0.7866 (p) cc_final: 0.7522 (t) REVERT: A 386 MET cc_start: 0.6631 (ttp) cc_final: 0.6308 (ttm) REVERT: A 400 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8403 (ttt) REVERT: A 435 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8267 (pp) REVERT: A 437 ARG cc_start: 0.8420 (mtt90) cc_final: 0.7897 (mtm180) REVERT: A 690 TYR cc_start: 0.5845 (m-80) cc_final: 0.5514 (m-80) REVERT: A 705 MET cc_start: 0.6223 (tpp) cc_final: 0.5964 (ttm) REVERT: A 761 MET cc_start: 0.6335 (tmm) cc_final: 0.6069 (tmm) REVERT: A 815 ASP cc_start: 0.8436 (t0) cc_final: 0.8162 (t0) REVERT: C 165 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7674 (mm-30) outliers start: 43 outliers final: 20 residues processed: 120 average time/residue: 0.4041 time to fit residues: 54.3678 Evaluate side-chains 104 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 79 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 13 optimal weight: 0.0050 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 ASN A 888 HIS A1242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.149896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104856 restraints weight = 16090.192| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.69 r_work: 0.3467 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11820 Z= 0.115 Angle : 0.779 29.850 16023 Z= 0.337 Chirality : 0.043 0.223 1822 Planarity : 0.004 0.047 1996 Dihedral : 9.398 108.005 1663 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 2.79 % Allowed : 16.20 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1410 helix: 0.86 (0.22), residues: 591 sheet: -0.61 (0.35), residues: 202 loop : -1.39 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 543 TYR 0.016 0.001 TYR C 77 PHE 0.016 0.001 PHE A 709 TRP 0.022 0.001 TRP A1172 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11811) covalent geometry : angle 0.77781 / 0.34 (16001) SS BOND : bond 0.00345 / 0.25 ( 2) SS BOND : angle 1.34487 / 1.01 ( 4) hydrogen bonds : bond 0.03560 / 2.33 ( 494) hydrogen bonds : angle 4.16333 / 2.93 ( 1398) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : bond 0.00524 / 0.33 ( 3) link_BETA1-4 : angle 1.35304 / 0.87 ( 9) link_NAG-ASN : bond 0.00345 / 0.21 ( 3) link_NAG-ASN : angle 1.20339 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8200 (tttt) cc_final: 0.7821 (mmpt) REVERT: A 263 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.6139 (tmm) REVERT: A 277 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5950 (mmmt) REVERT: A 386 MET cc_start: 0.6860 (ttp) cc_final: 0.6574 (ttm) REVERT: A 400 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: A 435 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8263 (pp) REVERT: A 437 ARG cc_start: 0.8468 (mtt90) cc_final: 0.7862 (mtm180) REVERT: A 690 TYR cc_start: 0.5916 (m-80) cc_final: 0.5481 (m-80) REVERT: A 705 MET cc_start: 0.6230 (tpp) cc_final: 0.5985 (ttm) REVERT: A 761 MET cc_start: 0.6358 (tmm) cc_final: 0.6113 (tmm) REVERT: A 815 ASP cc_start: 0.8407 (t0) cc_final: 0.8123 (t0) REVERT: A 864 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 866 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7506 (tmm160) REVERT: A 1228 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7874 (tmt170) REVERT: C 165 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7664 (mm-30) outliers start: 35 outliers final: 15 residues processed: 118 average time/residue: 0.4404 time to fit residues: 57.9222 Evaluate side-chains 107 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.149272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.105444 restraints weight = 15743.969| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.58 r_work: 0.3478 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11820 Z= 0.118 Angle : 0.781 29.862 16023 Z= 0.336 Chirality : 0.043 0.212 1822 Planarity : 0.004 0.047 1996 Dihedral : 9.295 106.017 1663 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 3.43 % Allowed : 15.96 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1410 helix: 1.03 (0.23), residues: 586 sheet: -0.60 (0.35), residues: 203 loop : -1.34 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 543 TYR 0.015 0.001 TYR C 77 PHE 0.018 0.001 PHE A 626 TRP 0.027 0.001 TRP A1172 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11811) covalent geometry : angle 0.77987 / 0.34 (16001) SS BOND : bond 0.00315 / 0.22 ( 2) SS BOND : angle 1.33718 / 1.02 ( 4) hydrogen bonds : bond 0.03531 / 2.31 ( 494) hydrogen bonds : angle 4.13874 / 2.92 ( 1398) Misc. bond : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : bond 0.00453 / 0.29 ( 3) link_BETA1-4 : angle 1.32042 / 0.87 ( 9) link_NAG-ASN : bond 0.00370 / 0.23 ( 3) link_NAG-ASN : angle 1.15546 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8327 (tttt) cc_final: 0.7930 (mmpt) REVERT: A 263 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.6153 (tmm) REVERT: A 277 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5955 (mmmt) REVERT: A 386 MET cc_start: 0.6894 (ttp) cc_final: 0.6626 (ttm) REVERT: A 400 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8261 (ttt) REVERT: A 435 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8291 (pp) REVERT: A 437 ARG cc_start: 0.8397 (mtt90) cc_final: 0.7777 (mtm180) REVERT: A 690 TYR cc_start: 0.6060 (m-80) cc_final: 0.5584 (m-80) REVERT: A 705 MET cc_start: 0.6273 (tpp) cc_final: 0.5914 (ptm) REVERT: A 761 MET cc_start: 0.6446 (tmm) cc_final: 0.6190 (tmm) REVERT: A 815 ASP cc_start: 0.8407 (t0) cc_final: 0.8117 (t0) REVERT: A 866 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7511 (tmm160) REVERT: A 1172 TRP cc_start: 0.7871 (t-100) cc_final: 0.7624 (t-100) REVERT: A 1228 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7830 (tmt170) REVERT: C 165 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7642 (mm-30) outliers start: 43 outliers final: 16 residues processed: 120 average time/residue: 0.4404 time to fit residues: 58.8364 Evaluate side-chains 106 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.147326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.102395 restraints weight = 16243.912| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.67 r_work: 0.3428 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11820 Z= 0.181 Angle : 0.823 30.196 16023 Z= 0.362 Chirality : 0.046 0.219 1822 Planarity : 0.004 0.049 1996 Dihedral : 9.489 107.216 1663 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 2.87 % Allowed : 17.16 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1410 helix: 0.83 (0.22), residues: 589 sheet: -0.57 (0.36), residues: 192 loop : -1.48 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 272 TYR 0.015 0.002 TYR C 141 PHE 0.038 0.002 PHE A 626 TRP 0.021 0.001 TRP A1172 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (11811) covalent geometry : angle 0.82154 / 0.36 (16001) SS BOND : bond 0.00498 / 0.36 ( 2) SS BOND : angle 1.67366 / 1.31 ( 4) hydrogen bonds : bond 0.04052 / 2.66 ( 494) hydrogen bonds : angle 4.26563 / 3.02 ( 1398) Misc. bond : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : bond 0.00413 / 0.27 ( 3) link_BETA1-4 : angle 1.47596 / 1.02 ( 9) link_NAG-ASN : bond 0.00401 / 0.23 ( 3) link_NAG-ASN : angle 1.26796 / 0.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8298 (tttt) cc_final: 0.7907 (mmpt) REVERT: A 263 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6107 (tmm) REVERT: A 277 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5988 (mmmt) REVERT: A 386 MET cc_start: 0.6869 (ttp) cc_final: 0.6541 (ttm) REVERT: A 400 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (ttt) REVERT: A 435 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (pp) REVERT: A 437 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7794 (mtm180) REVERT: A 652 SER cc_start: 0.7369 (t) cc_final: 0.6308 (p) REVERT: A 690 TYR cc_start: 0.5848 (m-80) cc_final: 0.5370 (m-80) REVERT: A 705 MET cc_start: 0.6221 (tpp) cc_final: 0.5871 (ptm) REVERT: A 761 MET cc_start: 0.6347 (tmm) cc_final: 0.6119 (tmm) REVERT: A 815 ASP cc_start: 0.8453 (t0) cc_final: 0.8152 (t0) REVERT: A 1228 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7931 (tmt170) REVERT: C 165 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7688 (mm-30) outliers start: 36 outliers final: 18 residues processed: 108 average time/residue: 0.4522 time to fit residues: 54.3113 Evaluate side-chains 105 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.0070 chunk 125 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.147779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103071 restraints weight = 16116.474| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.62 r_work: 0.3442 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11820 Z= 0.154 Angle : 0.811 30.071 16023 Z= 0.354 Chirality : 0.045 0.218 1822 Planarity : 0.004 0.048 1996 Dihedral : 9.479 107.507 1663 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 2.39 % Allowed : 18.04 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1410 helix: 0.90 (0.22), residues: 589 sheet: -0.47 (0.37), residues: 193 loop : -1.47 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 272 TYR 0.014 0.001 TYR C 141 PHE 0.024 0.001 PHE A 626 TRP 0.032 0.001 TRP A1172 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (11811) covalent geometry : angle 0.80962 / 0.35 (16001) SS BOND : bond 0.00411 / 0.29 ( 2) SS BOND : angle 1.55831 / 1.20 ( 4) hydrogen bonds : bond 0.03868 / 2.53 ( 494) hydrogen bonds : angle 4.26157 / 3.01 ( 1398) Misc. bond : bond 0.00009 / 0.01 ( 1) link_BETA1-4 : bond 0.00483 / 0.31 ( 3) link_BETA1-4 : angle 1.39725 / 0.93 ( 9) link_NAG-ASN : bond 0.00373 / 0.22 ( 3) link_NAG-ASN : angle 1.26331 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8225 (tttt) cc_final: 0.7822 (mmpt) REVERT: A 263 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.6023 (tmm) REVERT: A 277 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5817 (mmmt) REVERT: A 386 MET cc_start: 0.6656 (ttp) cc_final: 0.6313 (ttm) REVERT: A 400 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8389 (ttt) REVERT: A 435 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8373 (pp) REVERT: A 437 ARG cc_start: 0.8442 (mtt90) cc_final: 0.7813 (mtm180) REVERT: A 652 SER cc_start: 0.7278 (t) cc_final: 0.6202 (p) REVERT: A 690 TYR cc_start: 0.5728 (m-80) cc_final: 0.5318 (m-80) REVERT: A 698 PHE cc_start: 0.6117 (t80) cc_final: 0.5758 (t80) REVERT: A 705 MET cc_start: 0.6179 (tpp) cc_final: 0.5840 (ptm) REVERT: A 761 MET cc_start: 0.6265 (tmm) cc_final: 0.6030 (tmm) REVERT: A 815 ASP cc_start: 0.8443 (t0) cc_final: 0.8143 (t0) REVERT: A 1228 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7920 (tmt170) REVERT: C 143 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8756 (mm) REVERT: C 165 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7653 (mm-30) outliers start: 30 outliers final: 18 residues processed: 108 average time/residue: 0.4649 time to fit residues: 55.7133 Evaluate side-chains 105 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.150934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106455 restraints weight = 16165.823| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.70 r_work: 0.3477 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11820 Z= 0.110 Angle : 0.801 29.708 16023 Z= 0.348 Chirality : 0.043 0.244 1822 Planarity : 0.004 0.047 1996 Dihedral : 9.285 106.896 1663 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 2.00 % Allowed : 18.60 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.23), residues: 1410 helix: 1.10 (0.23), residues: 592 sheet: -0.38 (0.36), residues: 214 loop : -1.31 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 272 TYR 0.016 0.001 TYR C 77 PHE 0.029 0.001 PHE A 709 TRP 0.038 0.001 TRP A1172 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (11811) covalent geometry : angle 0.80016 / 0.35 (16001) SS BOND : bond 0.00305 / 0.22 ( 2) SS BOND : angle 1.26303 / 0.96 ( 4) hydrogen bonds : bond 0.03436 / 2.24 ( 494) hydrogen bonds : angle 4.17797 / 2.94 ( 1398) Misc. bond : bond 0.00001 / 0.00 ( 1) link_BETA1-4 : bond 0.00491 / 0.31 ( 3) link_BETA1-4 : angle 1.26688 / 0.80 ( 9) link_NAG-ASN : bond 0.00328 / 0.20 ( 3) link_NAG-ASN : angle 1.20237 / 0.76 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7784 (m-40) REVERT: A 216 LYS cc_start: 0.8189 (tttt) cc_final: 0.7876 (mmpt) REVERT: A 263 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.6220 (tmm) REVERT: A 277 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5779 (mmmt) REVERT: A 386 MET cc_start: 0.6880 (ttp) cc_final: 0.6574 (ttm) REVERT: A 400 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8365 (ttt) REVERT: A 435 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8313 (pp) REVERT: A 437 ARG cc_start: 0.8429 (mtt90) cc_final: 0.7832 (mtm180) REVERT: A 652 SER cc_start: 0.7276 (t) cc_final: 0.6174 (p) REVERT: A 690 TYR cc_start: 0.5725 (m-80) cc_final: 0.5313 (m-80) REVERT: A 705 MET cc_start: 0.6224 (tpp) cc_final: 0.5907 (ptm) REVERT: A 761 MET cc_start: 0.6255 (tmm) cc_final: 0.6033 (tmm) REVERT: A 815 ASP cc_start: 0.8404 (t0) cc_final: 0.8090 (t0) REVERT: A 866 ARG cc_start: 0.7920 (ppt170) cc_final: 0.7566 (tmm160) REVERT: C 54 CYS cc_start: 0.8175 (t) cc_final: 0.7732 (t) REVERT: C 165 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7657 (mm-30) outliers start: 25 outliers final: 15 residues processed: 109 average time/residue: 0.4361 time to fit residues: 53.0153 Evaluate side-chains 104 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 93 optimal weight: 0.0170 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 HIS ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.149236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104615 restraints weight = 16336.292| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.69 r_work: 0.3451 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11820 Z= 0.149 Angle : 0.825 30.070 16023 Z= 0.362 Chirality : 0.044 0.238 1822 Planarity : 0.004 0.047 1996 Dihedral : 9.334 106.553 1663 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 1.84 % Allowed : 18.99 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1410 helix: 1.02 (0.22), residues: 588 sheet: -0.42 (0.36), residues: 210 loop : -1.40 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 272 TYR 0.013 0.001 TYR C 141 PHE 0.028 0.001 PHE A 709 TRP 0.040 0.001 TRP A1172 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (11811) covalent geometry : angle 0.82443 / 0.36 (16001) SS BOND : bond 0.00380 / 0.27 ( 2) SS BOND : angle 1.47615 / 1.14 ( 4) hydrogen bonds : bond 0.03768 / 2.45 ( 494) hydrogen bonds : angle 4.24845 / 3.01 ( 1398) Misc. bond : bond 0.00006 / 0.00 ( 1) link_BETA1-4 : bond 0.00507 / 0.33 ( 3) link_BETA1-4 : angle 1.38417 / 0.92 ( 9) link_NAG-ASN : bond 0.00389 / 0.23 ( 3) link_NAG-ASN : angle 1.21444 / 0.79 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.58 seconds wall clock time: 60 minutes 15.14 seconds (3615.14 seconds total)