Starting phenix.real_space_refine on Thu Aug 6 07:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7k_41984/08_2026/8u7k_41984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7k_41984/08_2026/8u7k_41984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u7k_41984/08_2026/8u7k_41984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7k_41984/08_2026/8u7k_41984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7k_41984/08_2026/8u7k_41984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7k_41984/08_2026/8u7k_41984.map" } resolution = 4.1 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= 0.018 sd= 0.098 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 63 5.16 5 C 9247 2.51 5 N 2278 2.21 5 O 2557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 6863 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 9, 'GLU:plan': 12, 'ASN:plan1': 1, 'TYR:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 6863 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 9, 'GLU:plan': 12, 'ASN:plan1': 1, 'TYR:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 3.41, per 1000 atoms: 0.24 Number of scatterers: 14147 At special positions: 0 Unit cell: (111.78, 111.78, 133.86, 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 63 16.00 P 2 15.00 O 2557 8.00 N 2278 7.00 C 9247 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: 1.31 Conformation dependent library (CDL) restraints added in 705.0 milliseconds 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3404 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 8 sheets defined 74.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.802A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.652A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 removed outlier: 4.052A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.618A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.672A pdb=" N ALA A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 224 through 254 Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.245A 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: 3.690A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.840A pdb=" N LEU A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 414 removed outlier: 3.644A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.579A pdb=" N TRP A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.586A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.134A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.985A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 4.260A pdb=" N LEU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 520' Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.752A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 621 removed outlier: 4.153A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.727A pdb=" N GLN A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.645A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 854 removed outlier: 3.731A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.175A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 954 through 958 Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1081 removed outlier: 4.170A pdb=" N THR A1081 " --> pdb=" O ILE A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1105 removed outlier: 3.791A pdb=" N ILE A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A1100 " --> pdb=" O ILE A1096 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1122 Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.670A pdb=" N LYS B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.821A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.755A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 removed outlier: 3.895A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix removed outlier: 3.597A pdb=" N ALA B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.595A pdb=" N ALA B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 224 through 254 Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.241A 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 297 through 319 removed outlier: 3.696A pdb=" N ILE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 4.075A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 376 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 381 through 414 removed outlier: 3.693A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.565A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 482 removed outlier: 4.199A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 4.018A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 4.290A pdb=" N LEU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP B 520 " --> pdb=" O PHE B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 520' Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.785A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 601 Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.842A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.547A pdb=" N GLN B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 removed outlier: 3.670A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 854 removed outlier: 3.728A pdb=" N LYS B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 860 through 889 Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.207A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 966 through 975 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1081 removed outlier: 4.168A pdb=" N THR B1081 " --> pdb=" O ILE B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1105 removed outlier: 3.785A pdb=" N ILE B1098 " --> pdb=" O VAL B1094 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B1100 " --> pdb=" O ILE B1096 " (cutoff:3.500A) Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1122 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 4.166A pdb=" N ASN A1040 " --> pdb=" O ILE A1001 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 5.258A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 7.471A pdb=" N ARG A1185 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU A1147 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A1187 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A1145 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A1189 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 4.168A pdb=" N ASN B1040 " --> pdb=" O ILE B1001 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 5.262A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 7.472A pdb=" N ARG B1185 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU B1147 " --> pdb=" O ARG B1185 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B1187 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B1145 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B1189 " --> pdb=" O GLU B1143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137 1042 hydrogen bonds defined for protein. 3078 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: 2.40 Time building geometry restraints manager: 1.72 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: 2365 1.32 - 1.45: 3585 1.45 - 1.57: 8382 1.57 - 1.69: 4 1.69 - 1.82: 114 Bond restraints: 14450 Sorted by residual: bond pdb=" CG1 ILE A 844 " pdb=" CD1 ILE A 844 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 bond pdb=" C26 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.375 1.409 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C45 AJP B1401 " pdb=" O44 AJP B1401 " ideal model delta sigma weight residual 1.375 1.409 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C23 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.423 1.456 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C65 AJP A1404 " pdb=" O64 AJP A1404 " ideal model delta sigma weight residual 1.373 1.406 -0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 14445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 19034 2.20 - 4.39: 555 4.39 - 6.59: 88 6.59 - 8.79: 35 8.79 - 10.98: 18 Bond angle restraints: 19730 Sorted by residual: angle pdb=" N TRP A 635 " pdb=" CA TRP A 635 " pdb=" C TRP A 635 " ideal model delta sigma weight residual 111.36 115.54 -4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N GLN B 597 " pdb=" CA GLN B 597 " pdb=" CB GLN B 597 " ideal model delta sigma weight residual 110.22 116.07 -5.85 1.54e+00 4.22e-01 1.44e+01 angle pdb=" N GLN A 597 " pdb=" CA GLN A 597 " pdb=" CB GLN A 597 " ideal model delta sigma weight residual 110.28 116.15 -5.87 1.55e+00 4.16e-01 1.43e+01 angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 107.43 6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA GLN A 597 " pdb=" CB GLN A 597 " pdb=" CG GLN A 597 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.71: 8621 27.71 - 55.43: 383 55.43 - 83.14: 49 83.14 - 110.85: 56 110.85 - 138.57: 16 Dihedral angle restraints: 9125 sinusoidal: 3873 harmonic: 5252 Sorted by residual: dihedral pdb=" O31 AJP A1404 " pdb=" C30 AJP A1404 " pdb=" C32 AJP A1404 " pdb=" O33 AJP A1404 " ideal model delta sinusoidal sigma weight residual 177.28 38.71 138.57 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C29 AJP A1404 " pdb=" C30 AJP A1404 " pdb=" C32 AJP A1404 " pdb=" O33 AJP A1404 " ideal model delta sinusoidal sigma weight residual 299.04 162.74 136.30 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA TYR B 102 " pdb=" C TYR B 102 " pdb=" N THR B 103 " pdb=" CA THR B 103 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2064 0.066 - 0.132: 357 0.132 - 0.199: 37 0.199 - 0.265: 7 0.265 - 0.331: 2 Chirality restraints: 2467 Sorted by residual: chirality pdb=" C11 AJP B1401 " pdb=" C10 AJP B1401 " pdb=" C12 AJP B1401 " pdb=" C16 AJP B1401 " both_signs ideal model delta sigma weight residual False 2.20 2.54 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C2' CMP A1405 " pdb=" C1' CMP A1405 " pdb=" C3' CMP A1405 " pdb=" O2' CMP A1405 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2' CMP B1404 " pdb=" C1' CMP B1404 " pdb=" C3' CMP B1404 " pdb=" O2' CMP B1404 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2464 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 889 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO B 890 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 890 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 890 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 594 " 0.010 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR A 594 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 594 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 594 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 594 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 594 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 594 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 594 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 635 " -0.009 2.00e-02 2.50e+03 1.39e-02 4.82e+00 pdb=" CG TRP B 635 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 635 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 635 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 635 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 635 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 635 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 635 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 635 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 635 " 0.002 2.00e-02 2.50e+03 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 912 2.73 - 3.27: 15237 3.27 - 3.81: 23978 3.81 - 4.36: 25192 4.36 - 4.90: 42766 Nonbonded interactions: 108085 Sorted by model distance: nonbonded pdb=" O43 AJP A1404 " pdb=" O75 AJP A1404 " model vdw 2.182 3.040 nonbonded pdb=" OG SER A 593 " pdb=" OE1 GLU A 849 " model vdw 2.254 3.040 nonbonded pdb=" O LEU B 220 " pdb=" OG SER B 484 " model vdw 2.288 3.040 nonbonded pdb=" O LEU B 610 " pdb=" ND1 HIS B 614 " model vdw 2.295 3.120 nonbonded pdb=" O SER A 404 " pdb=" OG SER A 407 " model vdw 2.304 3.040 ... (remaining 108080 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 1004 or (resid 1005 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1006 through 1191 or (resid 1402 and (nam \ e C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or n \ ame C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name O21 or name O22 or name O31 or name O32 or name C210 or name C211 or \ name C212 or name C213 or name C214)) or resid 1403)) selection = (chain 'B' and (resid 76 through 424 or (resid 425 and (name N or name CA or nam \ e C or name O or name CB )) or resid 426 through 1191 or (resid 1402 and (name C \ 1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name O21 or name O22 or name O31 or name O32 or name C210 or name C211 or nam \ e C212 or name C213 or name C214)) 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.170 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 0.067 14450 Z= 0.223 Angle : 0.939 10.982 19730 Z= 0.444 Chirality : 0.051 0.331 2467 Planarity : 0.005 0.087 2377 Dihedral : 18.773 138.565 5721 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1796 helix: 0.81 (0.14), residues: 1262 sheet: 0.22 (0.50), residues: 110 loop : -0.49 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 875 TYR 0.046 0.002 TYR A 594 PHE 0.036 0.002 PHE B 455 TRP 0.036 0.002 TRP B 635 HIS 0.014 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (14450) covalent geometry : angle 0.93934 / 0.44 (19730) hydrogen bonds : bond 0.11604 / 7.86 ( 1042) hydrogen bonds : angle 5.35362 / 3.87 ( 3078) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8615 (pmm) cc_final: 0.8344 (pmm) REVERT: A 199 MET cc_start: 0.8519 (ttt) cc_final: 0.8100 (ttt) REVERT: A 201 PHE cc_start: 0.9118 (t80) cc_final: 0.8598 (t80) REVERT: A 205 MET cc_start: 0.8054 (mpp) cc_final: 0.7404 (mpp) REVERT: A 231 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 240 CYS cc_start: 0.8777 (m) cc_final: 0.8302 (m) REVERT: A 268 PHE cc_start: 0.8614 (t80) cc_final: 0.8231 (t80) REVERT: A 524 ASP cc_start: 0.8967 (p0) cc_final: 0.8388 (p0) REVERT: A 586 MET cc_start: 0.8452 (ptp) cc_final: 0.8061 (ptp) REVERT: A 643 TRP cc_start: 0.6789 (t60) cc_final: 0.6255 (t-100) REVERT: B 231 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8154 (mt-10) REVERT: B 240 CYS cc_start: 0.8779 (m) cc_final: 0.8307 (m) REVERT: B 268 PHE cc_start: 0.8594 (t80) cc_final: 0.8216 (t80) REVERT: B 370 VAL cc_start: 0.9397 (p) cc_final: 0.9113 (t) REVERT: B 524 ASP cc_start: 0.9008 (p0) cc_final: 0.8464 (p0) REVERT: B 586 MET cc_start: 0.8400 (ptp) cc_final: 0.8069 (ptp) REVERT: B 924 GLU cc_start: 0.8601 (pp20) cc_final: 0.8257 (pp20) REVERT: B 925 MET cc_start: 0.9091 (mmp) cc_final: 0.8852 (mmm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1020 time to fit residues: 47.3059 Evaluate side-chains 226 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.0970 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074477 restraints weight = 44024.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074508 restraints weight = 36299.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074785 restraints weight = 33266.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075441 restraints weight = 23284.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075581 restraints weight = 21347.927| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14450 Z= 0.154 Angle : 0.722 8.146 19730 Z= 0.342 Chirality : 0.042 0.253 2467 Planarity : 0.004 0.059 2377 Dihedral : 13.811 126.621 2752 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1796 helix: 1.33 (0.14), residues: 1290 sheet: 0.16 (0.48), residues: 110 loop : -0.62 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 875 TYR 0.027 0.002 TYR A 309 PHE 0.022 0.001 PHE B 455 TRP 0.059 0.002 TRP B 635 HIS 0.003 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14450) covalent geometry : angle 0.72228 / 0.34 (19730) hydrogen bonds : bond 0.05154 / 3.45 ( 1042) hydrogen bonds : angle 4.24163 / 3.09 ( 3078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8524 (pmm) cc_final: 0.8249 (pmm) REVERT: A 199 MET cc_start: 0.8342 (ttt) cc_final: 0.7886 (ttt) REVERT: A 240 CYS cc_start: 0.8744 (m) cc_final: 0.8306 (m) REVERT: A 268 PHE cc_start: 0.8474 (t80) cc_final: 0.8088 (t80) REVERT: A 366 MET cc_start: 0.7743 (ttm) cc_final: 0.7477 (ttm) REVERT: A 401 MET cc_start: 0.8943 (ptm) cc_final: 0.8662 (ptm) REVERT: A 524 ASP cc_start: 0.9079 (p0) cc_final: 0.8350 (p0) REVERT: A 586 MET cc_start: 0.8338 (ptp) cc_final: 0.7953 (ptp) REVERT: A 633 LYS cc_start: 0.9455 (pttp) cc_final: 0.9179 (pttm) REVERT: A 643 TRP cc_start: 0.6757 (t60) cc_final: 0.6367 (t-100) REVERT: A 853 ILE cc_start: 0.9083 (tp) cc_final: 0.8811 (tp) REVERT: B 160 MET cc_start: 0.8018 (ptm) cc_final: 0.7719 (ptt) REVERT: B 233 GLU cc_start: 0.8272 (tp30) cc_final: 0.7994 (tp30) REVERT: B 240 CYS cc_start: 0.8637 (m) cc_final: 0.8224 (m) REVERT: B 268 PHE cc_start: 0.8514 (t80) cc_final: 0.8115 (t80) REVERT: B 524 ASP cc_start: 0.9164 (p0) cc_final: 0.8508 (p0) REVERT: B 578 MET cc_start: 0.8392 (ppp) cc_final: 0.8177 (ppp) REVERT: B 586 MET cc_start: 0.8331 (ptp) cc_final: 0.7993 (ptp) REVERT: B 588 LYS cc_start: 0.9351 (ptpp) cc_final: 0.9132 (pttm) REVERT: B 597 GLN cc_start: 0.8710 (mp10) cc_final: 0.8475 (mp10) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.0936 time to fit residues: 43.9071 Evaluate side-chains 227 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 88 optimal weight: 30.0000 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 144 optimal weight: 0.0970 chunk 123 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075585 restraints weight = 44050.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075149 restraints weight = 32731.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075651 restraints weight = 29686.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076214 restraints weight = 21047.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076390 restraints weight = 19784.749| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14450 Z= 0.122 Angle : 0.674 9.834 19730 Z= 0.316 Chirality : 0.040 0.237 2467 Planarity : 0.004 0.047 2377 Dihedral : 11.313 100.531 2752 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1796 helix: 1.49 (0.14), residues: 1290 sheet: 0.21 (0.47), residues: 110 loop : -0.56 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 875 TYR 0.022 0.001 TYR A 309 PHE 0.018 0.001 PHE B 406 TRP 0.066 0.002 TRP B 635 HIS 0.014 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (14450) covalent geometry : angle 0.67409 / 0.32 (19730) hydrogen bonds : bond 0.04516 / 3.01 ( 1042) hydrogen bonds : angle 3.99796 / 2.92 ( 3078) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8394 (ttt) cc_final: 0.7910 (ttt) REVERT: A 233 GLU cc_start: 0.8389 (tp30) cc_final: 0.8104 (tp30) REVERT: A 240 CYS cc_start: 0.8752 (m) cc_final: 0.8348 (m) REVERT: A 268 PHE cc_start: 0.8553 (t80) cc_final: 0.8197 (t80) REVERT: A 366 MET cc_start: 0.7764 (ttm) cc_final: 0.7354 (ttm) REVERT: A 401 MET cc_start: 0.8967 (ptm) cc_final: 0.8661 (ptm) REVERT: A 524 ASP cc_start: 0.9142 (p0) cc_final: 0.8466 (p0) REVERT: A 586 MET cc_start: 0.8429 (ptp) cc_final: 0.8093 (ptp) REVERT: A 590 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 597 GLN cc_start: 0.8612 (mp10) cc_final: 0.8316 (mp10) REVERT: A 853 ILE cc_start: 0.9109 (tp) cc_final: 0.8828 (tp) REVERT: B 160 MET cc_start: 0.8173 (ptm) cc_final: 0.7856 (ptt) REVERT: B 233 GLU cc_start: 0.8530 (tp30) cc_final: 0.8158 (tp30) REVERT: B 240 CYS cc_start: 0.8695 (m) cc_final: 0.8268 (m) REVERT: B 268 PHE cc_start: 0.8614 (t80) cc_final: 0.8249 (t80) REVERT: B 524 ASP cc_start: 0.9173 (p0) cc_final: 0.8511 (p0) REVERT: B 578 MET cc_start: 0.8510 (ppp) cc_final: 0.8293 (ppp) REVERT: B 586 MET cc_start: 0.8470 (ptp) cc_final: 0.8066 (ptp) REVERT: B 597 GLN cc_start: 0.8722 (mp10) cc_final: 0.8369 (mp10) REVERT: B 633 LYS cc_start: 0.9451 (pttm) cc_final: 0.9234 (pttm) REVERT: B 853 ILE cc_start: 0.9238 (tp) cc_final: 0.8926 (tp) REVERT: B 912 THR cc_start: 0.9132 (t) cc_final: 0.8800 (t) REVERT: B 938 MET cc_start: 0.8739 (tpt) cc_final: 0.8526 (tpt) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.0934 time to fit residues: 45.7528 Evaluate side-chains 249 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 2 optimal weight: 0.0870 chunk 174 optimal weight: 40.0000 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.103082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075127 restraints weight = 44665.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074413 restraints weight = 38043.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074930 restraints weight = 34909.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075228 restraints weight = 23913.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.075641 restraints weight = 21828.250| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14450 Z= 0.142 Angle : 0.681 8.956 19730 Z= 0.322 Chirality : 0.041 0.243 2467 Planarity : 0.004 0.044 2377 Dihedral : 10.584 90.927 2752 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.20), residues: 1796 helix: 1.57 (0.14), residues: 1292 sheet: 0.19 (0.47), residues: 110 loop : -0.50 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 875 TYR 0.026 0.001 TYR A 309 PHE 0.013 0.001 PHE B 248 TRP 0.063 0.002 TRP B 635 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14450) covalent geometry : angle 0.68131 / 0.32 (19730) hydrogen bonds : bond 0.04467 / 2.98 ( 1042) hydrogen bonds : angle 4.00775 / 2.93 ( 3078) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8359 (pmm) cc_final: 0.7688 (pmm) REVERT: A 199 MET cc_start: 0.8444 (ttt) cc_final: 0.8135 (ttt) REVERT: A 233 GLU cc_start: 0.8378 (tp30) cc_final: 0.8017 (tp30) REVERT: A 240 CYS cc_start: 0.8734 (m) cc_final: 0.8348 (m) REVERT: A 366 MET cc_start: 0.7600 (ttm) cc_final: 0.7372 (ttm) REVERT: A 401 MET cc_start: 0.8964 (ptm) cc_final: 0.8638 (ptm) REVERT: A 524 ASP cc_start: 0.9138 (p0) cc_final: 0.8389 (p0) REVERT: A 586 MET cc_start: 0.8404 (ptp) cc_final: 0.8016 (ptp) REVERT: A 594 TYR cc_start: 0.9512 (m-80) cc_final: 0.9039 (m-80) REVERT: A 614 HIS cc_start: 0.8472 (m90) cc_final: 0.8160 (m90) REVERT: A 633 LYS cc_start: 0.9354 (pttp) cc_final: 0.8855 (mtpt) REVERT: A 643 TRP cc_start: 0.6839 (t60) cc_final: 0.6404 (t-100) REVERT: A 853 ILE cc_start: 0.9087 (tp) cc_final: 0.8818 (tp) REVERT: B 160 MET cc_start: 0.8193 (ptm) cc_final: 0.7939 (ptt) REVERT: B 233 GLU cc_start: 0.8571 (tp30) cc_final: 0.8337 (tp30) REVERT: B 240 CYS cc_start: 0.8658 (m) cc_final: 0.8252 (m) REVERT: B 268 PHE cc_start: 0.8611 (t80) cc_final: 0.8234 (t80) REVERT: B 462 ILE cc_start: 0.9292 (tp) cc_final: 0.9027 (mm) REVERT: B 524 ASP cc_start: 0.9159 (p0) cc_final: 0.8452 (p0) REVERT: B 578 MET cc_start: 0.8518 (ppp) cc_final: 0.8295 (ppp) REVERT: B 586 MET cc_start: 0.8423 (ptp) cc_final: 0.8157 (ptt) REVERT: B 588 LYS cc_start: 0.9397 (ptpp) cc_final: 0.9165 (pttm) REVERT: B 853 ILE cc_start: 0.9225 (tp) cc_final: 0.8920 (tp) REVERT: B 912 THR cc_start: 0.9179 (t) cc_final: 0.8830 (t) REVERT: B 942 MET cc_start: 0.8675 (mmm) cc_final: 0.8350 (mmm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.0726 time to fit residues: 35.2997 Evaluate side-chains 243 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 12 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.103570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075592 restraints weight = 44245.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075552 restraints weight = 39273.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075742 restraints weight = 34784.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076356 restraints weight = 23532.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076511 restraints weight = 21908.028| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14450 Z= 0.126 Angle : 0.672 9.426 19730 Z= 0.317 Chirality : 0.041 0.269 2467 Planarity : 0.003 0.042 2377 Dihedral : 9.902 84.204 2752 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.20), residues: 1796 helix: 1.57 (0.14), residues: 1294 sheet: 0.19 (0.47), residues: 108 loop : -0.48 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 865 TYR 0.023 0.001 TYR A 309 PHE 0.012 0.001 PHE B 95 TRP 0.055 0.002 TRP A 635 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (14450) covalent geometry : angle 0.67223 / 0.32 (19730) hydrogen bonds : bond 0.04339 / 2.88 ( 1042) hydrogen bonds : angle 3.94800 / 2.88 ( 3078) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8423 (ttt) cc_final: 0.8036 (ttt) REVERT: A 233 GLU cc_start: 0.8561 (tp30) cc_final: 0.8183 (tp30) REVERT: A 240 CYS cc_start: 0.8754 (m) cc_final: 0.8354 (m) REVERT: A 366 MET cc_start: 0.7528 (ttm) cc_final: 0.7312 (ttm) REVERT: A 401 MET cc_start: 0.8960 (ptm) cc_final: 0.8635 (ptm) REVERT: A 524 ASP cc_start: 0.9142 (p0) cc_final: 0.8401 (p0) REVERT: A 586 MET cc_start: 0.8360 (ptp) cc_final: 0.8088 (ptp) REVERT: A 590 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 643 TRP cc_start: 0.6852 (t60) cc_final: 0.6345 (t-100) REVERT: A 853 ILE cc_start: 0.9104 (tp) cc_final: 0.8816 (tp) REVERT: A 938 MET cc_start: 0.8633 (tpt) cc_final: 0.8421 (tpt) REVERT: B 160 MET cc_start: 0.8237 (ptm) cc_final: 0.7981 (ptt) REVERT: B 233 GLU cc_start: 0.8420 (tp30) cc_final: 0.8147 (tp30) REVERT: B 240 CYS cc_start: 0.8681 (m) cc_final: 0.8257 (m) REVERT: B 268 PHE cc_start: 0.8583 (t80) cc_final: 0.8226 (t80) REVERT: B 524 ASP cc_start: 0.9158 (p0) cc_final: 0.8455 (p0) REVERT: B 586 MET cc_start: 0.8463 (ptp) cc_final: 0.8178 (ptt) REVERT: B 588 LYS cc_start: 0.9419 (ptpp) cc_final: 0.9178 (pttm) REVERT: B 853 ILE cc_start: 0.9179 (tp) cc_final: 0.8857 (tp) REVERT: B 912 THR cc_start: 0.9142 (t) cc_final: 0.8832 (t) REVERT: B 923 ASP cc_start: 0.7073 (t0) cc_final: 0.6828 (t0) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.0813 time to fit residues: 41.0635 Evaluate side-chains 255 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074724 restraints weight = 44829.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.074201 restraints weight = 32428.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074846 restraints weight = 27067.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075411 restraints weight = 20057.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075551 restraints weight = 19105.139| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14450 Z= 0.124 Angle : 0.678 9.045 19730 Z= 0.319 Chirality : 0.041 0.289 2467 Planarity : 0.004 0.050 2377 Dihedral : 9.481 78.360 2752 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.20), residues: 1796 helix: 1.65 (0.14), residues: 1294 sheet: 0.23 (0.48), residues: 108 loop : -0.46 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 865 TYR 0.022 0.001 TYR A 309 PHE 0.017 0.001 PHE B 365 TRP 0.087 0.002 TRP B 635 HIS 0.003 0.000 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (14450) covalent geometry : angle 0.67776 / 0.32 (19730) hydrogen bonds : bond 0.04246 / 2.81 ( 1042) hydrogen bonds : angle 3.91094 / 2.85 ( 3078) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8525 (ttt) cc_final: 0.8108 (ttt) REVERT: A 233 GLU cc_start: 0.8570 (tp30) cc_final: 0.8314 (tp30) REVERT: A 240 CYS cc_start: 0.8755 (m) cc_final: 0.8365 (m) REVERT: A 366 MET cc_start: 0.7633 (ttm) cc_final: 0.7361 (ttm) REVERT: A 401 MET cc_start: 0.9028 (ptm) cc_final: 0.8675 (ptm) REVERT: A 524 ASP cc_start: 0.9169 (p0) cc_final: 0.8468 (p0) REVERT: A 586 MET cc_start: 0.8435 (ptp) cc_final: 0.8097 (ptp) REVERT: A 590 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 633 LYS cc_start: 0.9378 (pttp) cc_final: 0.8919 (mtpt) REVERT: A 853 ILE cc_start: 0.9167 (tp) cc_final: 0.8868 (tp) REVERT: A 942 MET cc_start: 0.8615 (mmm) cc_final: 0.8398 (mmm) REVERT: B 124 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7239 (mp0) REVERT: B 160 MET cc_start: 0.8284 (ptm) cc_final: 0.8010 (ptt) REVERT: B 233 GLU cc_start: 0.8619 (tp30) cc_final: 0.8282 (tp30) REVERT: B 240 CYS cc_start: 0.8734 (m) cc_final: 0.8322 (m) REVERT: B 268 PHE cc_start: 0.8677 (t80) cc_final: 0.8311 (t80) REVERT: B 524 ASP cc_start: 0.9176 (p0) cc_final: 0.8517 (p0) REVERT: B 586 MET cc_start: 0.8505 (ptp) cc_final: 0.8133 (tmm) REVERT: B 588 LYS cc_start: 0.9456 (ptpp) cc_final: 0.9214 (pttm) REVERT: B 590 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 853 ILE cc_start: 0.9211 (tp) cc_final: 0.8888 (tp) REVERT: B 912 THR cc_start: 0.9118 (t) cc_final: 0.8812 (t) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.0892 time to fit residues: 45.1630 Evaluate side-chains 259 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 159 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.103515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.073887 restraints weight = 45184.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.072758 restraints weight = 34077.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.073636 restraints weight = 28213.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074052 restraints weight = 20799.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074241 restraints weight = 20264.430| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14450 Z= 0.139 Angle : 0.698 9.598 19730 Z= 0.331 Chirality : 0.041 0.299 2467 Planarity : 0.004 0.042 2377 Dihedral : 9.206 71.751 2752 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1796 helix: 1.64 (0.14), residues: 1296 sheet: 0.21 (0.47), residues: 108 loop : -0.54 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 865 TYR 0.023 0.001 TYR A 309 PHE 0.021 0.001 PHE B 406 TRP 0.066 0.002 TRP A 635 HIS 0.004 0.000 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14450) covalent geometry : angle 0.69773 / 0.33 (19730) hydrogen bonds : bond 0.04311 / 2.87 ( 1042) hydrogen bonds : angle 3.96113 / 2.88 ( 3078) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8491 (ttt) cc_final: 0.8074 (ttt) REVERT: A 233 GLU cc_start: 0.8628 (tp30) cc_final: 0.8359 (tp30) REVERT: A 240 CYS cc_start: 0.8815 (m) cc_final: 0.8420 (m) REVERT: A 366 MET cc_start: 0.7689 (ttm) cc_final: 0.7417 (ttm) REVERT: A 383 MET cc_start: 0.8362 (tmm) cc_final: 0.7881 (tmm) REVERT: A 401 MET cc_start: 0.9041 (ptm) cc_final: 0.8693 (ptm) REVERT: A 524 ASP cc_start: 0.9217 (p0) cc_final: 0.8576 (p0) REVERT: A 586 MET cc_start: 0.8524 (ptp) cc_final: 0.8119 (ptp) REVERT: A 590 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8381 (mt-10) REVERT: A 635 TRP cc_start: 0.7966 (p90) cc_final: 0.7337 (p90) REVERT: A 838 ASP cc_start: 0.8959 (t0) cc_final: 0.8731 (t0) REVERT: A 853 ILE cc_start: 0.9209 (tp) cc_final: 0.8918 (tp) REVERT: A 899 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7802 (ttm-80) REVERT: A 911 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 923 ASP cc_start: 0.7320 (t0) cc_final: 0.6802 (t0) REVERT: B 160 MET cc_start: 0.8360 (ptm) cc_final: 0.8077 (ptt) REVERT: B 233 GLU cc_start: 0.8548 (tp30) cc_final: 0.8184 (tp30) REVERT: B 240 CYS cc_start: 0.8788 (m) cc_final: 0.8360 (m) REVERT: B 268 PHE cc_start: 0.8711 (t80) cc_final: 0.8356 (t80) REVERT: B 524 ASP cc_start: 0.9199 (p0) cc_final: 0.8565 (p0) REVERT: B 586 MET cc_start: 0.8522 (ptp) cc_final: 0.8200 (ptt) REVERT: B 588 LYS cc_start: 0.9478 (ptpp) cc_final: 0.9244 (pttm) REVERT: B 838 ASP cc_start: 0.9037 (t0) cc_final: 0.8827 (t0) REVERT: B 853 ILE cc_start: 0.9273 (tp) cc_final: 0.8950 (tp) REVERT: B 912 THR cc_start: 0.9148 (t) cc_final: 0.8817 (t) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.0890 time to fit residues: 43.3005 Evaluate side-chains 250 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 120 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 129 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073482 restraints weight = 44244.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074238 restraints weight = 32923.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074526 restraints weight = 28198.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.074446 restraints weight = 19988.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074635 restraints weight = 18905.802| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14450 Z= 0.179 Angle : 0.729 8.381 19730 Z= 0.349 Chirality : 0.042 0.290 2467 Planarity : 0.004 0.052 2377 Dihedral : 9.224 68.317 2752 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1796 helix: 1.58 (0.14), residues: 1294 sheet: 0.15 (0.47), residues: 108 loop : -0.46 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 585 TYR 0.030 0.002 TYR A 387 PHE 0.015 0.001 PHE A 245 TRP 0.052 0.002 TRP A 635 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (14450) covalent geometry : angle 0.72938 / 0.35 (19730) hydrogen bonds : bond 0.04600 / 3.05 ( 1042) hydrogen bonds : angle 4.05971 / 2.96 ( 3078) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8485 (ttt) cc_final: 0.8083 (ttt) REVERT: A 233 GLU cc_start: 0.8544 (tp30) cc_final: 0.8250 (tp30) REVERT: A 240 CYS cc_start: 0.8829 (m) cc_final: 0.8417 (m) REVERT: A 366 MET cc_start: 0.7766 (ttm) cc_final: 0.7565 (ttm) REVERT: A 387 TYR cc_start: 0.7481 (m-80) cc_final: 0.6964 (m-80) REVERT: A 401 MET cc_start: 0.9008 (ptm) cc_final: 0.8668 (ptm) REVERT: A 524 ASP cc_start: 0.9202 (p0) cc_final: 0.8577 (p0) REVERT: A 586 MET cc_start: 0.8456 (ptp) cc_final: 0.8109 (ptp) REVERT: A 590 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8386 (mt-10) REVERT: A 635 TRP cc_start: 0.7969 (p90) cc_final: 0.7355 (p90) REVERT: A 643 TRP cc_start: 0.7004 (t60) cc_final: 0.6534 (t-100) REVERT: A 853 ILE cc_start: 0.9174 (tp) cc_final: 0.8879 (tp) REVERT: A 899 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7904 (ttm170) REVERT: A 923 ASP cc_start: 0.7546 (t0) cc_final: 0.7300 (t0) REVERT: B 160 MET cc_start: 0.8299 (ptm) cc_final: 0.8023 (ptt) REVERT: B 233 GLU cc_start: 0.8439 (tp30) cc_final: 0.8031 (tp30) REVERT: B 240 CYS cc_start: 0.8822 (m) cc_final: 0.8379 (m) REVERT: B 268 PHE cc_start: 0.8688 (t80) cc_final: 0.8336 (t80) REVERT: B 483 MET cc_start: 0.8451 (pmm) cc_final: 0.8226 (pmm) REVERT: B 524 ASP cc_start: 0.9201 (p0) cc_final: 0.8578 (p0) REVERT: B 586 MET cc_start: 0.8505 (ptp) cc_final: 0.8238 (ptt) REVERT: B 588 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9248 (pttm) REVERT: B 643 TRP cc_start: 0.6972 (t-100) cc_final: 0.6751 (t-100) REVERT: B 853 ILE cc_start: 0.9219 (tp) cc_final: 0.8903 (tp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.0919 time to fit residues: 43.2328 Evaluate side-chains 243 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074778 restraints weight = 44181.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075406 restraints weight = 32497.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075732 restraints weight = 24950.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075518 restraints weight = 17909.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075674 restraints weight = 17572.837| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14450 Z= 0.176 Angle : 0.740 10.852 19730 Z= 0.356 Chirality : 0.042 0.288 2467 Planarity : 0.004 0.047 2377 Dihedral : 9.162 65.570 2752 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 1796 helix: 1.54 (0.14), residues: 1296 sheet: 0.08 (0.47), residues: 108 loop : -0.48 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 583 TYR 0.028 0.002 TYR A 309 PHE 0.015 0.001 PHE B 148 TRP 0.104 0.002 TRP B 635 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (14450) covalent geometry : angle 0.74032 / 0.36 (19730) hydrogen bonds : bond 0.04678 / 3.10 ( 1042) hydrogen bonds : angle 4.10422 / 2.98 ( 3078) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8476 (ttt) cc_final: 0.8066 (ttt) REVERT: A 233 GLU cc_start: 0.8535 (tp30) cc_final: 0.8250 (tp30) REVERT: A 240 CYS cc_start: 0.8818 (m) cc_final: 0.8408 (m) REVERT: A 366 MET cc_start: 0.7813 (ttm) cc_final: 0.7586 (ttm) REVERT: A 387 TYR cc_start: 0.7214 (m-80) cc_final: 0.6723 (m-80) REVERT: A 401 MET cc_start: 0.8966 (ptm) cc_final: 0.8632 (ptm) REVERT: A 524 ASP cc_start: 0.9211 (p0) cc_final: 0.8599 (p0) REVERT: A 586 MET cc_start: 0.8435 (ptp) cc_final: 0.8113 (ptp) REVERT: A 590 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8357 (mt-10) REVERT: A 643 TRP cc_start: 0.7007 (t60) cc_final: 0.6536 (t-100) REVERT: A 853 ILE cc_start: 0.9133 (tp) cc_final: 0.8828 (tp) REVERT: A 857 MET cc_start: 0.8914 (tpt) cc_final: 0.8168 (tmm) REVERT: A 899 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7943 (ttm170) REVERT: B 160 MET cc_start: 0.8310 (ptm) cc_final: 0.8033 (ptt) REVERT: B 233 GLU cc_start: 0.8479 (tp30) cc_final: 0.8077 (tp30) REVERT: B 240 CYS cc_start: 0.8850 (m) cc_final: 0.8414 (m) REVERT: B 268 PHE cc_start: 0.8642 (t80) cc_final: 0.8291 (t80) REVERT: B 483 MET cc_start: 0.8420 (pmm) cc_final: 0.8176 (pmm) REVERT: B 524 ASP cc_start: 0.9198 (p0) cc_final: 0.8616 (p0) REVERT: B 586 MET cc_start: 0.8512 (ptp) cc_final: 0.8225 (ptt) REVERT: B 588 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9265 (pttm) REVERT: B 590 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 853 ILE cc_start: 0.9225 (tp) cc_final: 0.8915 (tp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.0916 time to fit residues: 42.5192 Evaluate side-chains 241 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 chunk 98 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 7 optimal weight: 0.2980 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076848 restraints weight = 44140.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076774 restraints weight = 36618.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.077553 restraints weight = 30192.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077417 restraints weight = 21618.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.077797 restraints weight = 20963.675| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14450 Z= 0.127 Angle : 0.732 10.748 19730 Z= 0.345 Chirality : 0.042 0.305 2467 Planarity : 0.004 0.044 2377 Dihedral : 8.589 62.784 2752 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1796 helix: 1.62 (0.14), residues: 1292 sheet: 0.17 (0.47), residues: 108 loop : -0.44 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 865 TYR 0.022 0.001 TYR A 387 PHE 0.021 0.001 PHE B 248 TRP 0.092 0.002 TRP A 635 HIS 0.003 0.000 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (14450) covalent geometry : angle 0.73194 / 0.34 (19730) hydrogen bonds : bond 0.04334 / 2.88 ( 1042) hydrogen bonds : angle 3.98351 / 2.90 ( 3078) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8333 (pmm) cc_final: 0.8094 (pmm) REVERT: A 199 MET cc_start: 0.8377 (ttt) cc_final: 0.8118 (ttt) REVERT: A 233 GLU cc_start: 0.8369 (tp30) cc_final: 0.7901 (tp30) REVERT: A 240 CYS cc_start: 0.8714 (m) cc_final: 0.8304 (m) REVERT: A 268 PHE cc_start: 0.8503 (t80) cc_final: 0.8140 (t80) REVERT: A 366 MET cc_start: 0.7664 (ttm) cc_final: 0.7418 (ttm) REVERT: A 387 TYR cc_start: 0.7253 (m-80) cc_final: 0.6877 (m-80) REVERT: A 401 MET cc_start: 0.8874 (ptm) cc_final: 0.8547 (ptm) REVERT: A 524 ASP cc_start: 0.9154 (p0) cc_final: 0.8455 (p0) REVERT: A 586 MET cc_start: 0.8333 (ptp) cc_final: 0.8043 (ptp) REVERT: A 590 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 633 LYS cc_start: 0.9404 (pttp) cc_final: 0.9073 (pttm) REVERT: A 843 TYR cc_start: 0.8896 (t80) cc_final: 0.8644 (t80) REVERT: A 847 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 853 ILE cc_start: 0.9079 (tp) cc_final: 0.8752 (tp) REVERT: A 857 MET cc_start: 0.8880 (tpt) cc_final: 0.8213 (tmm) REVERT: A 899 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7865 (ttm170) REVERT: B 160 MET cc_start: 0.8182 (ptm) cc_final: 0.7936 (ptt) REVERT: B 233 GLU cc_start: 0.8300 (tp30) cc_final: 0.7919 (tp30) REVERT: B 235 LEU cc_start: 0.9277 (tp) cc_final: 0.9071 (tp) REVERT: B 240 CYS cc_start: 0.8678 (m) cc_final: 0.8278 (m) REVERT: B 268 PHE cc_start: 0.8643 (t80) cc_final: 0.8295 (t80) REVERT: B 483 MET cc_start: 0.8402 (pmm) cc_final: 0.7944 (pmm) REVERT: B 524 ASP cc_start: 0.9164 (p0) cc_final: 0.8491 (p0) REVERT: B 586 MET cc_start: 0.8398 (ptp) cc_final: 0.8091 (ptp) REVERT: B 590 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 853 ILE cc_start: 0.9109 (tp) cc_final: 0.8765 (tp) REVERT: B 882 LEU cc_start: 0.9605 (mt) cc_final: 0.9240 (mt) REVERT: B 912 THR cc_start: 0.9121 (t) cc_final: 0.8837 (t) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.0874 time to fit residues: 43.5425 Evaluate side-chains 253 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 177 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 928 HIS ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075284 restraints weight = 44854.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.076588 restraints weight = 38379.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076411 restraints weight = 31087.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076100 restraints weight = 22842.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076363 restraints weight = 20644.979| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14450 Z= 0.163 Angle : 0.768 15.680 19730 Z= 0.372 Chirality : 0.043 0.296 2467 Planarity : 0.004 0.055 2377 Dihedral : 8.563 63.065 2752 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.20), residues: 1796 helix: 1.56 (0.14), residues: 1292 sheet: 0.18 (0.47), residues: 108 loop : -0.44 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 865 TYR 0.025 0.001 TYR A 309 PHE 0.032 0.002 PHE B 365 TRP 0.093 0.003 TRP A 635 HIS 0.004 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (14450) covalent geometry : angle 0.76757 / 0.37 (19730) hydrogen bonds : bond 0.04664 / 3.07 ( 1042) hydrogen bonds : angle 4.08004 / 2.97 ( 3078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.45 seconds wall clock time: 33 minutes 52.08 seconds (2032.08 seconds total)