Starting phenix.real_space_refine on Sat Jun 14 11:04:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u71_41965/06_2025/8u71_41965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u71_41965/06_2025/8u71_41965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u71_41965/06_2025/8u71_41965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u71_41965/06_2025/8u71_41965.map" model { file = "/net/cci-nas-00/data/ceres_data/8u71_41965/06_2025/8u71_41965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u71_41965/06_2025/8u71_41965.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 82 5.16 5 C 10501 2.51 5 N 2606 2.21 5 O 2842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16033 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7847 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 965} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 7847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7847 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 965} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 9.71, per 1000 atoms: 0.61 Number of scatterers: 16033 At special positions: 0 Unit cell: (106.7, 136.4, 124.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 2 15.00 O 2842 8.00 N 2606 7.00 C 10501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 2.0 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3748 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 76.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.562A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.773A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 154 removed outlier: 3.605A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 4.542A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 162 through 190 removed outlier: 3.618A pdb=" N VAL A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.677A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 4.106A pdb=" N SER A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.051A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.576A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 4.311A pdb=" N LEU A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 412 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.818A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.327A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 485 removed outlier: 3.522A pdb=" N ASP A 485 " --> pdb=" O GLY A 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 485' Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 514 through 515 No H-bonds generated for 'chain 'A' and resid 514 through 515' Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.909A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 677 through 699 removed outlier: 4.095A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 732 through 756 Processing helix chain 'A' and resid 762 through 776 Processing helix chain 'A' and resid 799 through 806 Processing helix chain 'A' and resid 807 through 812 Processing helix chain 'A' and resid 813 through 856 Proline residue: A 819 - end of helix removed outlier: 3.759A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 4.185A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.956A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 944 removed outlier: 3.759A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1124 removed outlier: 3.734A pdb=" N GLY A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.454A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.847A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 154 removed outlier: 3.650A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix removed outlier: 4.055A pdb=" N MET B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.803A pdb=" N PHE B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.638A pdb=" N VAL B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.764A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 4.126A pdb=" N SER B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.097A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 298 through 319 removed outlier: 3.636A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 4.273A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 381 through 412 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.849A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.267A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 removed outlier: 3.507A pdb=" N ASP B 485 " --> pdb=" O GLY B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 514 through 515 No H-bonds generated for 'chain 'B' and resid 514 through 515' Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.893A pdb=" N ALA B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP B 520 " --> pdb=" O PHE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 571 through 601 Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 677 through 699 removed outlier: 4.163A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 732 through 755 Processing helix chain 'B' and resid 762 through 776 Processing helix chain 'B' and resid 799 through 805 Processing helix chain 'B' and resid 807 through 812 Processing helix chain 'B' and resid 813 through 855 Proline residue: B 819 - end of helix removed outlier: 3.804A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 840 " --> pdb=" O GLY B 836 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 4.189A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.976A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 944 removed outlier: 3.776A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 977 Processing helix chain 'B' and resid 1044 through 1049 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1124 removed outlier: 3.870A pdb=" N GLY B1124 " --> pdb=" O HIS B1120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.314A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 999 " --> pdb=" O ILE A1042 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1033 through 1037 Processing sheet with id=AA3, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA4, first strand: chain 'A' and resid 1165 through 1166 removed outlier: 3.658A pdb=" N CYS A1165 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A1147 " --> pdb=" O CYS A1165 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A1189 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A1145 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A1187 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A1147 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG A1185 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.428A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 999 " --> pdb=" O ILE B1042 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1033 through 1036 Processing sheet with id=AA7, first strand: chain 'B' and resid 1135 through 1137 Processing sheet with id=AA8, first strand: chain 'B' and resid 1165 through 1166 removed outlier: 3.654A pdb=" N CYS B1165 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B1147 " --> pdb=" O CYS B1165 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1189 " --> pdb=" O GLU B1143 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B1145 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B1187 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU B1147 " --> pdb=" O ARG B1185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ARG B1185 " --> pdb=" O LEU B1147 " (cutoff:3.500A) 1143 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2715 1.32 - 1.45: 4017 1.45 - 1.57: 9481 1.57 - 1.69: 4 1.69 - 1.81: 150 Bond restraints: 16367 Sorted by residual: bond pdb=" CA ALA B 529 " pdb=" C ALA B 529 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.27e-02 6.20e+03 2.41e+00 bond pdb=" C26 AJP B1404 " pdb=" O25 AJP B1404 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C26 AJP A1402 " pdb=" O25 AJP A1402 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C26 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.375 1.404 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C26 AJP B1403 " pdb=" O25 AJP B1403 " ideal model delta sigma weight residual 1.375 1.403 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 16362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 21774 2.35 - 4.71: 368 4.71 - 7.06: 78 7.06 - 9.42: 17 9.42 - 11.77: 3 Bond angle restraints: 22240 Sorted by residual: angle pdb=" CB MET A 857 " pdb=" CG MET A 857 " pdb=" SD MET A 857 " ideal model delta sigma weight residual 112.70 124.47 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CB MET B 857 " pdb=" CG MET B 857 " pdb=" SD MET B 857 " ideal model delta sigma weight residual 112.70 123.18 -10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET A 511 " pdb=" CG MET A 511 " pdb=" SD MET A 511 " ideal model delta sigma weight residual 112.70 122.23 -9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET B 511 " pdb=" CG MET B 511 " pdb=" SD MET B 511 " ideal model delta sigma weight residual 112.70 122.12 -9.42 3.00e+00 1.11e-01 9.85e+00 angle pdb=" C VAL A 213 " pdb=" CA VAL A 213 " pdb=" CB VAL A 213 " ideal model delta sigma weight residual 112.02 107.93 4.09 1.31e+00 5.83e-01 9.76e+00 ... (remaining 22235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 9520 24.46 - 48.91: 617 48.91 - 73.37: 75 73.37 - 97.82: 11 97.82 - 122.28: 21 Dihedral angle restraints: 10244 sinusoidal: 4462 harmonic: 5782 Sorted by residual: dihedral pdb=" C55 AJP A1402 " pdb=" C59 AJP A1402 " pdb=" O60 AJP A1402 " pdb=" C58 AJP A1402 " ideal model delta sinusoidal sigma weight residual -60.14 62.14 -122.28 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C59 AJP A1402 " pdb=" C55 AJP A1402 " pdb=" O60 AJP A1402 " pdb=" O54 AJP A1402 " ideal model delta sinusoidal sigma weight residual 177.58 59.00 118.58 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C02 AJP B1403 " pdb=" C85 AJP B1403 " pdb=" O84 AJP B1403 " pdb=" C05 AJP B1403 " ideal model delta sinusoidal sigma weight residual -57.60 59.51 -117.11 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 10241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1883 0.042 - 0.083: 612 0.083 - 0.125: 177 0.125 - 0.167: 23 0.167 - 0.208: 19 Chirality restraints: 2714 Sorted by residual: chirality pdb=" C55 AJP A1402 " pdb=" C56 AJP A1402 " pdb=" O54 AJP A1402 " pdb=" O60 AJP A1402 " both_signs ideal model delta sigma weight residual False 2.13 2.33 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C55 AJP A1403 " pdb=" C56 AJP A1403 " pdb=" O54 AJP A1403 " pdb=" O60 AJP A1403 " both_signs ideal model delta sigma weight residual False 2.13 2.33 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C10 AJP A1402 " pdb=" C08 AJP A1402 " pdb=" C11 AJP A1402 " pdb=" O82 AJP A1402 " both_signs ideal model delta sigma weight residual False 2.61 2.40 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2711 not shown) Planarity restraints: 2680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO B 642 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO A 642 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 635 " -0.011 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP A 635 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 635 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 635 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 635 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 635 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 635 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 635 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 635 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 635 " 0.001 2.00e-02 2.50e+03 ... (remaining 2677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3545 2.79 - 3.31: 16196 3.31 - 3.84: 26401 3.84 - 4.37: 27110 4.37 - 4.90: 48414 Nonbonded interactions: 121666 Sorted by model distance: nonbonded pdb=" O VAL B 123 " pdb=" OG1 THR B 127 " model vdw 2.257 3.040 nonbonded pdb=" O VAL A 123 " pdb=" OG1 THR A 127 " model vdw 2.267 3.040 nonbonded pdb=" O62 AJP B1403 " pdb=" O63 AJP B1403 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU A 954 " pdb=" OH TYR A1066 " model vdw 2.294 3.040 nonbonded pdb=" O TYR B1153 " pdb=" OG1 THR B1175 " model vdw 2.298 3.040 ... (remaining 121661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 1192 or (resid 1401 and (name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or n \ ame C311 or name C312 or name C313 or name C314 or name C315)) or resid 1403)) selection = (chain 'B' and (resid 76 through 1192 or (resid 1401 and (name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or n \ ame C311 or name C312 or name C313 or name C314 or name C315)) or resid 1403)) } 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 group one per residue 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: 1.460 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.610 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16367 Z= 0.207 Angle : 0.785 11.771 22240 Z= 0.378 Chirality : 0.047 0.208 2714 Planarity : 0.004 0.076 2680 Dihedral : 16.221 122.278 6496 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.06 % Allowed : 0.29 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1966 helix: 1.19 (0.14), residues: 1442 sheet: 0.65 (0.49), residues: 120 loop : -1.32 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 635 HIS 0.004 0.001 HIS B 908 PHE 0.025 0.002 PHE A 201 TYR 0.015 0.001 TYR B 309 ARG 0.004 0.000 ARG A 809 Details of bonding type rmsd hydrogen bonds : bond 0.11285 ( 1143) hydrogen bonds : angle 4.86138 ( 3372) covalent geometry : bond 0.00451 (16367) covalent geometry : angle 0.78463 (22240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7182 (ptt) cc_final: 0.6536 (ptt) REVERT: A 273 VAL cc_start: 0.8509 (m) cc_final: 0.8286 (m) REVERT: A 530 CYS cc_start: 0.7732 (t) cc_final: 0.7256 (t) REVERT: B 530 CYS cc_start: 0.7620 (t) cc_final: 0.7162 (p) REVERT: B 579 MET cc_start: 0.8347 (tmm) cc_final: 0.8122 (tmm) REVERT: B 810 MET cc_start: 0.7340 (mmt) cc_final: 0.7032 (tmm) REVERT: B 857 MET cc_start: 0.8529 (tmm) cc_final: 0.8261 (ttm) REVERT: B 931 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7596 (tm-30) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.2568 time to fit residues: 56.3866 Evaluate side-chains 112 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 7.9990 chunk 150 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 955 ASN A1064 GLN B1064 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.098709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078422 restraints weight = 53305.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078706 restraints weight = 40049.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079355 restraints weight = 33572.481| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16367 Z= 0.121 Angle : 0.587 8.333 22240 Z= 0.288 Chirality : 0.037 0.187 2714 Planarity : 0.004 0.071 2680 Dihedral : 7.862 83.604 2838 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.24 % Allowed : 8.23 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 1966 helix: 1.75 (0.14), residues: 1448 sheet: 0.98 (0.50), residues: 118 loop : -1.00 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 635 HIS 0.003 0.001 HIS B 614 PHE 0.023 0.001 PHE B 201 TYR 0.014 0.001 TYR B 309 ARG 0.005 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1143) hydrogen bonds : angle 3.93534 ( 3372) covalent geometry : bond 0.00258 (16367) covalent geometry : angle 0.58726 (22240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8889 (mt) cc_final: 0.8591 (pp) REVERT: A 530 CYS cc_start: 0.7897 (t) cc_final: 0.7417 (t) REVERT: A 579 MET cc_start: 0.8204 (tmm) cc_final: 0.7908 (tmm) REVERT: A 641 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.6256 (m-80) REVERT: A 678 MET cc_start: 0.8051 (mmp) cc_final: 0.6893 (ppp) REVERT: A 1112 TRP cc_start: 0.7409 (m100) cc_final: 0.7152 (m100) REVERT: B 251 MET cc_start: 0.8589 (tmm) cc_final: 0.8167 (ttm) REVERT: B 492 LEU cc_start: 0.8884 (mt) cc_final: 0.8642 (pp) REVERT: B 579 MET cc_start: 0.8435 (tmm) cc_final: 0.8232 (tmm) REVERT: B 810 MET cc_start: 0.7355 (mmt) cc_final: 0.6959 (tmm) REVERT: B 931 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7571 (tm-30) outliers start: 4 outliers final: 1 residues processed: 125 average time/residue: 0.2333 time to fit residues: 47.8243 Evaluate side-chains 116 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 181 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.096921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.076678 restraints weight = 53429.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076714 restraints weight = 42012.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077301 restraints weight = 38511.229| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16367 Z= 0.165 Angle : 0.578 7.250 22240 Z= 0.290 Chirality : 0.038 0.139 2714 Planarity : 0.004 0.068 2680 Dihedral : 7.043 86.030 2838 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.41 % Allowed : 12.46 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 1966 helix: 1.96 (0.14), residues: 1456 sheet: 1.02 (0.51), residues: 118 loop : -0.94 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1112 HIS 0.004 0.001 HIS A 908 PHE 0.019 0.001 PHE B 365 TYR 0.013 0.001 TYR B 309 ARG 0.003 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 1143) hydrogen bonds : angle 3.86061 ( 3372) covalent geometry : bond 0.00375 (16367) covalent geometry : angle 0.57830 (22240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8914 (mt) cc_final: 0.8635 (pp) REVERT: A 579 MET cc_start: 0.8309 (tmm) cc_final: 0.8037 (tmm) REVERT: A 641 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: A 678 MET cc_start: 0.8117 (mmp) cc_final: 0.6910 (ppp) REVERT: A 1112 TRP cc_start: 0.7438 (m100) cc_final: 0.7124 (m100) REVERT: B 425 MET cc_start: 0.8927 (tmm) cc_final: 0.8718 (tmm) REVERT: B 492 LEU cc_start: 0.8908 (mt) cc_final: 0.8685 (pp) REVERT: B 578 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8816 (mpp) REVERT: B 579 MET cc_start: 0.8410 (tmm) cc_final: 0.8200 (tmm) REVERT: B 810 MET cc_start: 0.7283 (mmt) cc_final: 0.6870 (tmm) REVERT: B 931 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7579 (tm-30) outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.2251 time to fit residues: 44.8268 Evaluate side-chains 120 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 38 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.098540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078355 restraints weight = 53026.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.077844 restraints weight = 42070.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078912 restraints weight = 34178.978| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16367 Z= 0.109 Angle : 0.530 8.354 22240 Z= 0.263 Chirality : 0.036 0.145 2714 Planarity : 0.004 0.067 2680 Dihedral : 6.644 80.426 2838 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.82 % Allowed : 14.81 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.20), residues: 1966 helix: 2.05 (0.14), residues: 1460 sheet: 1.08 (0.52), residues: 108 loop : -0.97 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.002 0.000 HIS A 908 PHE 0.037 0.001 PHE B 248 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG A 809 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1143) hydrogen bonds : angle 3.71746 ( 3372) covalent geometry : bond 0.00230 (16367) covalent geometry : angle 0.53015 (22240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8878 (mt) cc_final: 0.8609 (pp) REVERT: A 578 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8816 (mpp) REVERT: A 579 MET cc_start: 0.8307 (tmm) cc_final: 0.8035 (tmm) REVERT: A 641 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: A 1112 TRP cc_start: 0.7336 (m100) cc_final: 0.7029 (m100) REVERT: B 251 MET cc_start: 0.8695 (tmm) cc_final: 0.8036 (ttm) REVERT: B 492 LEU cc_start: 0.8933 (mt) cc_final: 0.8684 (pp) REVERT: B 579 MET cc_start: 0.8456 (tmm) cc_final: 0.8194 (tmm) REVERT: B 810 MET cc_start: 0.7362 (mmt) cc_final: 0.6909 (tmm) REVERT: B 931 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7467 (tm-30) outliers start: 14 outliers final: 5 residues processed: 133 average time/residue: 0.2878 time to fit residues: 62.4576 Evaluate side-chains 121 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 68 optimal weight: 0.0060 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079187 restraints weight = 53412.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.080267 restraints weight = 44254.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080762 restraints weight = 35924.910| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16367 Z= 0.107 Angle : 0.535 9.223 22240 Z= 0.263 Chirality : 0.036 0.157 2714 Planarity : 0.003 0.066 2680 Dihedral : 6.383 76.628 2838 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.00 % Allowed : 16.98 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.20), residues: 1966 helix: 2.08 (0.14), residues: 1462 sheet: 1.09 (0.55), residues: 98 loop : -0.84 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.016 0.001 PHE B 201 TYR 0.011 0.001 TYR A 312 ARG 0.008 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 1143) hydrogen bonds : angle 3.65861 ( 3372) covalent geometry : bond 0.00231 (16367) covalent geometry : angle 0.53511 (22240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8864 (mt) cc_final: 0.8626 (pp) REVERT: A 579 MET cc_start: 0.8270 (tmm) cc_final: 0.7960 (tmm) REVERT: A 641 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: A 678 MET cc_start: 0.8060 (mmp) cc_final: 0.6949 (ppp) REVERT: A 1112 TRP cc_start: 0.7240 (m100) cc_final: 0.6939 (m100) REVERT: B 251 MET cc_start: 0.8816 (tmm) cc_final: 0.8010 (ttm) REVERT: B 492 LEU cc_start: 0.8912 (mt) cc_final: 0.8624 (pp) REVERT: B 810 MET cc_start: 0.7310 (mmt) cc_final: 0.6886 (tmm) REVERT: B 931 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7472 (tm-30) outliers start: 17 outliers final: 9 residues processed: 133 average time/residue: 0.2783 time to fit residues: 61.1816 Evaluate side-chains 129 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 181 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.098773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.078788 restraints weight = 53123.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.078793 restraints weight = 42798.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079778 restraints weight = 35347.627| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16367 Z= 0.111 Angle : 0.542 8.936 22240 Z= 0.268 Chirality : 0.036 0.186 2714 Planarity : 0.004 0.065 2680 Dihedral : 6.210 75.191 2838 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.18 % Allowed : 17.16 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1966 helix: 2.13 (0.14), residues: 1462 sheet: 1.12 (0.53), residues: 108 loop : -0.84 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.025 0.001 PHE A 201 TYR 0.011 0.001 TYR A 312 ARG 0.003 0.000 ARG B 875 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1143) hydrogen bonds : angle 3.65596 ( 3372) covalent geometry : bond 0.00243 (16367) covalent geometry : angle 0.54212 (22240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8867 (mt) cc_final: 0.8627 (pp) REVERT: A 641 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: A 678 MET cc_start: 0.7920 (mmp) cc_final: 0.7047 (ppp) REVERT: A 1112 TRP cc_start: 0.7133 (m100) cc_final: 0.6852 (m100) REVERT: B 492 LEU cc_start: 0.8917 (mt) cc_final: 0.8644 (pp) REVERT: B 810 MET cc_start: 0.7349 (mmt) cc_final: 0.6882 (tmm) REVERT: B 931 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7372 (tm-30) outliers start: 20 outliers final: 13 residues processed: 130 average time/residue: 0.2189 time to fit residues: 47.3471 Evaluate side-chains 132 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 133 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076167 restraints weight = 53535.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076096 restraints weight = 42410.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.076635 restraints weight = 38939.730| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16367 Z= 0.188 Angle : 0.611 9.199 22240 Z= 0.305 Chirality : 0.038 0.163 2714 Planarity : 0.004 0.064 2680 Dihedral : 6.490 81.769 2838 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.35 % Allowed : 17.74 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.20), residues: 1966 helix: 2.11 (0.14), residues: 1460 sheet: 1.01 (0.53), residues: 108 loop : -0.88 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 643 HIS 0.004 0.001 HIS A 908 PHE 0.026 0.002 PHE B 201 TYR 0.013 0.001 TYR A 309 ARG 0.002 0.000 ARG A 809 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 1143) hydrogen bonds : angle 3.79608 ( 3372) covalent geometry : bond 0.00434 (16367) covalent geometry : angle 0.61113 (22240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7493 (ptt) cc_final: 0.7288 (ptt) REVERT: A 492 LEU cc_start: 0.8914 (mt) cc_final: 0.8674 (pp) REVERT: A 641 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6102 (m-80) REVERT: A 1112 TRP cc_start: 0.7369 (m100) cc_final: 0.7042 (m100) REVERT: B 186 MET cc_start: 0.7011 (mmt) cc_final: 0.6785 (mmt) REVERT: B 300 GLU cc_start: 0.7877 (pm20) cc_final: 0.7417 (pt0) REVERT: B 492 LEU cc_start: 0.8897 (mt) cc_final: 0.8664 (pp) REVERT: B 810 MET cc_start: 0.7370 (mmt) cc_final: 0.6914 (tmm) REVERT: B 931 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7421 (tm-30) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 0.2386 time to fit residues: 51.5679 Evaluate side-chains 133 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 41 optimal weight: 0.0870 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.097591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.077386 restraints weight = 52781.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076420 restraints weight = 44869.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077514 restraints weight = 35611.208| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16367 Z= 0.129 Angle : 0.584 9.837 22240 Z= 0.285 Chirality : 0.037 0.172 2714 Planarity : 0.004 0.065 2680 Dihedral : 6.271 77.701 2838 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.41 % Allowed : 18.39 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.20), residues: 1966 helix: 2.15 (0.14), residues: 1460 sheet: 1.27 (0.54), residues: 104 loop : -0.82 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 643 HIS 0.003 0.000 HIS B 908 PHE 0.033 0.001 PHE A 201 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG B 809 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1143) hydrogen bonds : angle 3.70632 ( 3372) covalent geometry : bond 0.00290 (16367) covalent geometry : angle 0.58397 (22240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8929 (mt) cc_final: 0.8660 (pp) REVERT: A 641 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: A 678 MET cc_start: 0.7839 (mmp) cc_final: 0.6284 (ttt) REVERT: A 1112 TRP cc_start: 0.7229 (m100) cc_final: 0.6917 (m100) REVERT: B 492 LEU cc_start: 0.8894 (mt) cc_final: 0.8669 (pp) REVERT: B 810 MET cc_start: 0.7408 (mmt) cc_final: 0.6912 (tmm) REVERT: B 931 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7332 (tm-30) outliers start: 24 outliers final: 16 residues processed: 133 average time/residue: 0.2915 time to fit residues: 64.5999 Evaluate side-chains 131 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 172 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 45 optimal weight: 0.0020 chunk 131 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.099037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077984 restraints weight = 53103.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.077909 restraints weight = 34516.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078882 restraints weight = 27865.876| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16367 Z= 0.109 Angle : 0.583 11.646 22240 Z= 0.281 Chirality : 0.037 0.197 2714 Planarity : 0.004 0.066 2680 Dihedral : 5.929 68.870 2838 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.18 % Allowed : 18.68 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.20), residues: 1966 helix: 2.14 (0.14), residues: 1462 sheet: 1.33 (0.54), residues: 104 loop : -0.80 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.026 0.001 PHE B 201 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG A 809 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 1143) hydrogen bonds : angle 3.64476 ( 3372) covalent geometry : bond 0.00231 (16367) covalent geometry : angle 0.58335 (22240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8922 (mt) cc_final: 0.8651 (pp) REVERT: A 641 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: A 678 MET cc_start: 0.7832 (mmp) cc_final: 0.6248 (ttt) REVERT: B 186 MET cc_start: 0.6769 (mmt) cc_final: 0.6545 (mmt) REVERT: B 300 GLU cc_start: 0.7962 (pm20) cc_final: 0.7497 (pt0) REVERT: B 492 LEU cc_start: 0.8960 (mt) cc_final: 0.8636 (pp) REVERT: B 810 MET cc_start: 0.7479 (mmt) cc_final: 0.6932 (tmm) REVERT: B 931 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7320 (tm-30) outliers start: 20 outliers final: 16 residues processed: 133 average time/residue: 0.2298 time to fit residues: 51.4259 Evaluate side-chains 134 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 181 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.098573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078310 restraints weight = 53598.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077525 restraints weight = 44161.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078853 restraints weight = 34318.871| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16367 Z= 0.117 Angle : 0.592 11.299 22240 Z= 0.285 Chirality : 0.037 0.207 2714 Planarity : 0.004 0.065 2680 Dihedral : 5.874 67.524 2838 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.18 % Allowed : 19.10 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 1966 helix: 2.17 (0.14), residues: 1462 sheet: 1.29 (0.54), residues: 104 loop : -0.80 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.026 0.001 PHE B 201 TYR 0.011 0.001 TYR A 312 ARG 0.002 0.000 ARG B 809 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 1143) hydrogen bonds : angle 3.64419 ( 3372) covalent geometry : bond 0.00262 (16367) covalent geometry : angle 0.59196 (22240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8916 (mt) cc_final: 0.8655 (pp) REVERT: A 586 MET cc_start: 0.8777 (tpp) cc_final: 0.8074 (ttp) REVERT: A 641 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: A 678 MET cc_start: 0.7850 (mmp) cc_final: 0.6247 (ttt) REVERT: B 186 MET cc_start: 0.6676 (mmt) cc_final: 0.6456 (mmt) REVERT: B 206 SER cc_start: 0.8246 (m) cc_final: 0.8005 (m) REVERT: B 300 GLU cc_start: 0.7937 (pm20) cc_final: 0.7394 (pt0) REVERT: B 492 LEU cc_start: 0.8892 (mt) cc_final: 0.8618 (pp) REVERT: B 810 MET cc_start: 0.7438 (mmt) cc_final: 0.6843 (tmm) REVERT: B 931 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7318 (tm-30) outliers start: 20 outliers final: 18 residues processed: 131 average time/residue: 0.2233 time to fit residues: 48.7043 Evaluate side-chains 137 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 2 optimal weight: 0.0970 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.0010 chunk 181 optimal weight: 7.9990 chunk 159 optimal weight: 0.0970 chunk 162 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.098367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.078225 restraints weight = 53066.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077387 restraints weight = 44101.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.078430 restraints weight = 35001.576| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16367 Z= 0.122 Angle : 0.598 11.150 22240 Z= 0.287 Chirality : 0.037 0.182 2714 Planarity : 0.004 0.064 2680 Dihedral : 5.805 65.515 2838 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.29 % Allowed : 19.15 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.20), residues: 1966 helix: 2.18 (0.14), residues: 1462 sheet: 1.29 (0.54), residues: 104 loop : -0.80 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.027 0.001 PHE B 201 TYR 0.011 0.001 TYR A 312 ARG 0.002 0.000 ARG B 809 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1143) hydrogen bonds : angle 3.64473 ( 3372) covalent geometry : bond 0.00275 (16367) covalent geometry : angle 0.59808 (22240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4314.16 seconds wall clock time: 79 minutes 41.76 seconds (4781.76 seconds total)