Starting phenix.real_space_refine on Sun Aug 24 01:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u71_41965/08_2025/8u71_41965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u71_41965/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u71_41965/08_2025/8u71_41965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u71_41965/08_2025/8u71_41965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u71_41965/08_2025/8u71_41965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u71_41965/08_2025/8u71_41965.map" } resolution = 3.9 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= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.59, per 1000 atoms: 0.29 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: 1.76 Conformation dependent library (CDL) restraints added in 835.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.63 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: 3.40 Time building geometry restraints manager: 2.23 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.000 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.850 ------------------------------------------------------------------------------- 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 : 7.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 809 TYR 0.015 0.001 TYR B 309 PHE 0.025 0.002 PHE A 201 TRP 0.040 0.002 TRP A 635 HIS 0.004 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00451 (16367) covalent geometry : angle 0.78463 (22240) hydrogen bonds : bond 0.11285 ( 1143) hydrogen bonds : angle 4.86138 ( 3372) *********************** 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 : 0.660 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: 0.1150 time to fit residues: 25.1489 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 : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.099121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079129 restraints weight = 53221.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079556 restraints weight = 36924.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.079920 restraints weight = 32349.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080590 restraints weight = 23016.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080768 restraints weight = 20635.148| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0958 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= 0.115 Angle : 0.584 8.239 22240 Z= 0.284 Chirality : 0.037 0.187 2714 Planarity : 0.004 0.072 2680 Dihedral : 7.672 81.518 2838 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.72 (0.20), residues: 1966 helix: 1.74 (0.14), residues: 1448 sheet: 0.99 (0.50), residues: 118 loop : -0.99 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.013 0.001 TYR A 312 PHE 0.021 0.001 PHE B 201 TRP 0.027 0.001 TRP A 635 HIS 0.003 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00232 (16367) covalent geometry : angle 0.58381 (22240) hydrogen bonds : bond 0.04205 ( 1143) hydrogen bonds : angle 3.90294 ( 3372) *********************** 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 128 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8861 (mt) cc_final: 0.8554 (pp) REVERT: A 579 MET cc_start: 0.8220 (tmm) cc_final: 0.7895 (tmm) REVERT: A 641 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: A 678 MET cc_start: 0.8038 (mmp) cc_final: 0.6233 (ttt) REVERT: A 955 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8424 (t0) REVERT: B 492 LEU cc_start: 0.8852 (mt) cc_final: 0.8598 (pp) REVERT: B 579 MET cc_start: 0.8442 (tmm) cc_final: 0.8232 (tmm) REVERT: B 810 MET cc_start: 0.7455 (mmt) cc_final: 0.6996 (tmm) REVERT: B 931 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7556 (tm-30) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.1086 time to fit residues: 22.7789 Evaluate side-chains 118 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 955 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 163 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.099365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.079414 restraints weight = 53634.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.079819 restraints weight = 42838.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080436 restraints weight = 35347.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080862 restraints weight = 26112.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081194 restraints weight = 23947.080| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1149 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= 0.108 Angle : 0.537 8.278 22240 Z= 0.265 Chirality : 0.036 0.131 2714 Planarity : 0.004 0.067 2680 Dihedral : 6.776 79.011 2838 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.41 % Allowed : 11.63 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.99 (0.20), residues: 1966 helix: 1.94 (0.14), residues: 1458 sheet: 1.09 (0.51), residues: 118 loop : -1.00 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.011 0.001 TYR A 312 PHE 0.024 0.001 PHE B 201 TRP 0.019 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00225 (16367) covalent geometry : angle 0.53666 (22240) hydrogen bonds : bond 0.03939 ( 1143) hydrogen bonds : angle 3.75742 ( 3372) *********************** 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 128 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.757 Fit side-chains REVERT: A 492 LEU cc_start: 0.8872 (mt) cc_final: 0.8593 (pp) REVERT: A 530 CYS cc_start: 0.8521 (t) cc_final: 0.7532 (t) REVERT: A 579 MET cc_start: 0.8271 (tmm) cc_final: 0.7943 (tmm) REVERT: A 641 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: A 678 MET cc_start: 0.8116 (mmp) cc_final: 0.6953 (ppp) REVERT: A 1112 TRP cc_start: 0.7423 (m100) cc_final: 0.7052 (m100) REVERT: B 251 MET cc_start: 0.8749 (tmm) cc_final: 0.8078 (ttm) REVERT: B 492 LEU cc_start: 0.8911 (mt) cc_final: 0.8607 (pp) REVERT: B 578 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8819 (mpp) REVERT: B 579 MET cc_start: 0.8423 (tmm) cc_final: 0.8181 (tmm) REVERT: B 678 MET cc_start: 0.7843 (pmm) cc_final: 0.7629 (pmm) REVERT: B 810 MET cc_start: 0.7438 (mmt) cc_final: 0.6970 (tmm) REVERT: B 931 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7550 (tm-30) outliers start: 7 outliers final: 3 residues processed: 124 average time/residue: 0.1077 time to fit residues: 22.4157 Evaluate side-chains 124 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 1059 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 470 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.096009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.075829 restraints weight = 53445.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076017 restraints weight = 42221.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.076543 restraints weight = 37565.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076943 restraints weight = 26322.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077224 restraints weight = 24019.339| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16367 Z= 0.206 Angle : 0.603 7.599 22240 Z= 0.305 Chirality : 0.039 0.147 2714 Planarity : 0.004 0.066 2680 Dihedral : 6.994 86.896 2838 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.06 % Allowed : 14.63 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.09 (0.20), residues: 1966 helix: 2.02 (0.14), residues: 1454 sheet: 0.66 (0.51), residues: 124 loop : -0.81 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.015 0.001 TYR A 309 PHE 0.025 0.002 PHE B 201 TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00473 (16367) covalent geometry : angle 0.60311 (22240) hydrogen bonds : bond 0.04540 ( 1143) hydrogen bonds : angle 3.87298 ( 3372) *********************** 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 136 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8904 (mt) cc_final: 0.8652 (pp) REVERT: A 578 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8794 (mpp) REVERT: A 579 MET cc_start: 0.8302 (tmm) cc_final: 0.8072 (tmm) REVERT: A 641 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: A 810 MET cc_start: 0.7485 (mmt) cc_final: 0.7254 (mmt) REVERT: B 174 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 579 MET cc_start: 0.8421 (tmm) cc_final: 0.8197 (tmm) REVERT: B 810 MET cc_start: 0.7340 (mmt) cc_final: 0.6980 (tmm) REVERT: B 931 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7521 (tm-30) REVERT: B 1107 MET cc_start: 0.7659 (tpp) cc_final: 0.7256 (tpp) outliers start: 18 outliers final: 8 residues processed: 127 average time/residue: 0.1035 time to fit residues: 22.1490 Evaluate side-chains 123 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 941 LEU 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 144 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.098677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.078150 restraints weight = 53345.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077775 restraints weight = 39187.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078623 restraints weight = 31783.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078879 restraints weight = 23609.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.079078 restraints weight = 22398.679| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16367 Z= 0.111 Angle : 0.541 8.834 22240 Z= 0.267 Chirality : 0.036 0.152 2714 Planarity : 0.004 0.067 2680 Dihedral : 6.501 78.902 2838 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.88 % Allowed : 17.04 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.18 (0.20), residues: 1966 helix: 2.08 (0.14), residues: 1462 sheet: 1.06 (0.52), residues: 108 loop : -0.90 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 809 TYR 0.012 0.001 TYR A 312 PHE 0.024 0.001 PHE B 201 TRP 0.020 0.001 TRP A 643 HIS 0.002 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00239 (16367) covalent geometry : angle 0.54070 (22240) hydrogen bonds : bond 0.03918 ( 1143) hydrogen bonds : angle 3.68466 ( 3372) *********************** 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 137 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8887 (mt) cc_final: 0.8614 (pp) REVERT: A 579 MET cc_start: 0.8333 (tmm) cc_final: 0.8035 (tmm) REVERT: A 641 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: A 678 MET cc_start: 0.8154 (mmp) cc_final: 0.6392 (ttt) REVERT: A 1112 TRP cc_start: 0.7292 (m100) cc_final: 0.6987 (m100) REVERT: B 251 MET cc_start: 0.8606 (tmm) cc_final: 0.7926 (ttm) REVERT: B 678 MET cc_start: 0.7774 (pmm) cc_final: 0.7541 (pmm) REVERT: B 810 MET cc_start: 0.7405 (mmt) cc_final: 0.6908 (tmm) REVERT: B 931 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 15 outliers final: 6 residues processed: 132 average time/residue: 0.1121 time to fit residues: 24.3798 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 : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 640 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.097226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.076768 restraints weight = 53494.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077411 restraints weight = 39134.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.077599 restraints weight = 34849.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078146 restraints weight = 24526.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078323 restraints weight = 21983.338| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16367 Z= 0.155 Angle : 0.574 8.845 22240 Z= 0.287 Chirality : 0.037 0.181 2714 Planarity : 0.004 0.066 2680 Dihedral : 6.528 81.511 2838 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.29 % Allowed : 17.74 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.19 (0.20), residues: 1966 helix: 2.10 (0.14), residues: 1462 sheet: 0.65 (0.52), residues: 114 loop : -0.79 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 431 TYR 0.012 0.001 TYR B 309 PHE 0.020 0.001 PHE A 201 TRP 0.018 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00358 (16367) covalent geometry : angle 0.57390 (22240) hydrogen bonds : bond 0.04160 ( 1143) hydrogen bonds : angle 3.75842 ( 3372) *********************** 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 135 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8902 (mt) cc_final: 0.8661 (pp) REVERT: A 641 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: A 678 MET cc_start: 0.8052 (mmp) cc_final: 0.7064 (ppp) REVERT: A 1112 TRP cc_start: 0.7344 (m100) cc_final: 0.7028 (m100) REVERT: B 251 MET cc_start: 0.8658 (tmm) cc_final: 0.8012 (ttm) REVERT: B 492 LEU cc_start: 0.8897 (mt) cc_final: 0.8670 (pp) REVERT: B 810 MET cc_start: 0.7385 (mmt) cc_final: 0.6959 (tmm) REVERT: B 931 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7401 (tm-30) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 0.1084 time to fit residues: 23.0465 Evaluate side-chains 125 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 925 MET 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 144 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.097299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.076924 restraints weight = 53339.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077839 restraints weight = 38858.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.077970 restraints weight = 34314.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078604 restraints weight = 24046.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078789 restraints weight = 20992.463| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16367 Z= 0.144 Angle : 0.586 10.514 22240 Z= 0.288 Chirality : 0.037 0.158 2714 Planarity : 0.004 0.067 2680 Dihedral : 6.426 80.100 2838 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.41 % Allowed : 18.33 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.23 (0.20), residues: 1966 helix: 2.12 (0.14), residues: 1462 sheet: 0.86 (0.53), residues: 110 loop : -0.81 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 809 TYR 0.012 0.001 TYR A 312 PHE 0.024 0.001 PHE A 201 TRP 0.025 0.001 TRP B 643 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00332 (16367) covalent geometry : angle 0.58583 (22240) hydrogen bonds : bond 0.04119 ( 1143) hydrogen bonds : angle 3.73393 ( 3372) *********************** 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 137 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8911 (mt) cc_final: 0.8648 (pp) REVERT: A 641 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6166 (m-80) REVERT: A 678 MET cc_start: 0.7918 (mmp) cc_final: 0.7073 (ppp) REVERT: A 1112 TRP cc_start: 0.7241 (m100) cc_final: 0.6930 (m100) REVERT: B 251 MET cc_start: 0.8704 (tmm) cc_final: 0.8015 (ttm) REVERT: B 300 GLU cc_start: 0.7936 (pm20) cc_final: 0.7493 (pt0) REVERT: B 492 LEU cc_start: 0.8910 (mt) cc_final: 0.8698 (pp) REVERT: B 810 MET cc_start: 0.7368 (mmt) cc_final: 0.6912 (tmm) REVERT: B 931 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 24 outliers final: 17 residues processed: 126 average time/residue: 0.1026 time to fit residues: 21.8987 Evaluate side-chains 129 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR 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 850 VAL 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 213 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 925 MET 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 138 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 chunk 120 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 121 optimal weight: 0.0270 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.099284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079176 restraints weight = 53113.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080270 restraints weight = 38487.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080646 restraints weight = 30857.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080959 restraints weight = 22474.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.081133 restraints weight = 20737.942| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16367 Z= 0.106 Angle : 0.568 11.179 22240 Z= 0.275 Chirality : 0.036 0.153 2714 Planarity : 0.003 0.067 2680 Dihedral : 6.027 69.435 2838 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.23 % Allowed : 19.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.20), residues: 1966 helix: 2.13 (0.14), residues: 1462 sheet: 1.36 (0.54), residues: 104 loop : -0.85 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 809 TYR 0.012 0.001 TYR A 312 PHE 0.019 0.001 PHE A 201 TRP 0.023 0.001 TRP B 643 HIS 0.002 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00221 (16367) covalent geometry : angle 0.56797 (22240) hydrogen bonds : bond 0.03672 ( 1143) hydrogen bonds : angle 3.64595 ( 3372) *********************** 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 141 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8878 (mt) cc_final: 0.8647 (pp) REVERT: A 641 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: B 251 MET cc_start: 0.8634 (tmm) cc_final: 0.7980 (ttm) REVERT: B 810 MET cc_start: 0.7355 (mmt) cc_final: 0.6883 (tmm) REVERT: B 931 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7303 (tm-30) outliers start: 21 outliers final: 16 residues processed: 131 average time/residue: 0.1047 time to fit residues: 23.0709 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 : 0.641 ------------------------------------------------------------------------------- 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 483 MET 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 948 ILE 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 119 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.097392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.077123 restraints weight = 53511.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077528 restraints weight = 40138.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077979 restraints weight = 36002.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078149 restraints weight = 26235.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078452 restraints weight = 24129.719| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16367 Z= 0.148 Angle : 0.609 10.764 22240 Z= 0.297 Chirality : 0.037 0.201 2714 Planarity : 0.004 0.065 2680 Dihedral : 6.176 74.794 2838 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.23 % Allowed : 19.39 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.31 (0.20), residues: 1966 helix: 2.17 (0.14), residues: 1460 sheet: 1.32 (0.54), residues: 104 loop : -0.87 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 809 TYR 0.011 0.001 TYR A 312 PHE 0.019 0.001 PHE A 201 TRP 0.031 0.001 TRP A 643 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00340 (16367) covalent geometry : angle 0.60914 (22240) hydrogen bonds : bond 0.04043 ( 1143) hydrogen bonds : angle 3.70823 ( 3372) *********************** 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 134 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8908 (mt) cc_final: 0.8667 (pp) REVERT: A 641 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: A 678 MET cc_start: 0.7985 (mmp) cc_final: 0.6313 (ttt) REVERT: A 1112 TRP cc_start: 0.7130 (m100) cc_final: 0.6824 (m100) REVERT: B 251 MET cc_start: 0.8696 (tmm) cc_final: 0.7811 (ttm) REVERT: B 300 GLU cc_start: 0.7954 (pm20) cc_final: 0.7461 (pt0) REVERT: B 810 MET cc_start: 0.7435 (mmt) cc_final: 0.6953 (tmm) REVERT: B 931 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7329 (tm-30) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.1045 time to fit residues: 21.9696 Evaluate side-chains 127 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 367 MET 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 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 75 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 128 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 1.2180 ------------------------------------------------------------------------------- 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 = 0.098565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.078366 restraints weight = 53166.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.078911 restraints weight = 38641.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.079188 restraints weight = 34575.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.079772 restraints weight = 24711.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079977 restraints weight = 22079.532| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16367 Z= 0.118 Angle : 0.600 11.084 22240 Z= 0.288 Chirality : 0.037 0.184 2714 Planarity : 0.004 0.066 2680 Dihedral : 5.976 69.311 2838 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.29 % Allowed : 19.51 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.20), residues: 1966 helix: 2.15 (0.14), residues: 1460 sheet: 1.25 (0.54), residues: 104 loop : -0.87 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 809 TYR 0.011 0.001 TYR A 312 PHE 0.022 0.001 PHE B 248 TRP 0.034 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00263 (16367) covalent geometry : angle 0.60005 (22240) hydrogen bonds : bond 0.03817 ( 1143) hydrogen bonds : angle 3.66649 ( 3372) ********************** 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: 22 poor density : 117 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8902 (mt) cc_final: 0.8661 (pp) REVERT: A 641 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: A 678 MET cc_start: 0.8126 (mmp) cc_final: 0.6381 (ttt) REVERT: B 300 GLU cc_start: 0.7966 (pm20) cc_final: 0.7445 (pt0) REVERT: B 492 LEU cc_start: 0.8914 (mt) cc_final: 0.8694 (pp) REVERT: B 810 MET cc_start: 0.7408 (mmt) cc_final: 0.6895 (tmm) REVERT: B 931 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7292 (tm-30) outliers start: 22 outliers final: 18 residues processed: 129 average time/residue: 0.1080 time to fit residues: 23.4284 Evaluate side-chains 133 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 367 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 948 ILE 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 113 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 145 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.098731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078691 restraints weight = 52832.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.078456 restraints weight = 41252.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079342 restraints weight = 33862.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.079807 restraints weight = 24770.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080097 restraints weight = 22726.744| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16367 Z= 0.114 Angle : 0.606 10.756 22240 Z= 0.289 Chirality : 0.037 0.196 2714 Planarity : 0.004 0.066 2680 Dihedral : 5.804 66.124 2838 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.29 % Allowed : 19.74 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.27 (0.20), residues: 1966 helix: 2.14 (0.14), residues: 1462 sheet: 1.21 (0.54), residues: 104 loop : -0.85 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 809 TYR 0.011 0.001 TYR A 312 PHE 0.015 0.001 PHE A 201 TRP 0.037 0.001 TRP A 643 HIS 0.003 0.000 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00249 (16367) covalent geometry : angle 0.60560 (22240) hydrogen bonds : bond 0.03744 ( 1143) hydrogen bonds : angle 3.65237 ( 3372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.09 seconds wall clock time: 37 minutes 17.89 seconds (2237.89 seconds total)