Starting phenix.real_space_refine on Sat Oct 11 11:18:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7k_41984/10_2025/8u7k_41984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7k_41984/10_2025/8u7k_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_41984/10_2025/8u7k_41984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7k_41984/10_2025/8u7k_41984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7k_41984/10_2025/8u7k_41984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7k_41984/10_2025/8u7k_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-2.0-5842/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 3.58, per 1000 atoms: 0.25 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 440.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.43 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: 2.51 Time building geometry restraints manager: 1.59 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: 19040 2.20 - 4.39: 557 4.39 - 6.59: 88 6.59 - 8.79: 31 8.79 - 10.98: 14 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: 8619 27.71 - 55.43: 383 55.43 - 83.14: 49 83.14 - 110.85: 56 110.85 - 138.57: 18 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: 2066 0.066 - 0.132: 357 0.132 - 0.199: 37 0.199 - 0.265: 6 0.265 - 0.331: 1 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=" C08 AJP B1401 " pdb=" C07 AJP B1401 " pdb=" C10 AJP B1401 " pdb=" O09 AJP B1401 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C55 AJP B1401 " pdb=" C56 AJP B1401 " pdb=" O54 AJP B1401 " pdb=" O60 AJP B1401 " both_signs ideal model delta sigma weight residual False 2.13 2.37 -0.25 2.00e-01 2.50e+01 1.54e+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: 0.390 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.030 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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= 0.222 Angle : 0.923 10.982 19730 Z= 0.442 Chirality : 0.051 0.331 2467 Planarity : 0.005 0.087 2377 Dihedral : 18.927 138.565 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 aren 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 covalent geometry : bond 0.00485 (14450) covalent geometry : angle 0.92317 (19730) hydrogen bonds : bond 0.11604 ( 1042) hydrogen bonds : angle 5.35362 ( 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 : 0.537 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: 0.8573 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 240 CYS cc_start: 0.8778 (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: 0.8451 (ptp) cc_final: 0.8060 (ptp) REVERT: A 643 TRP cc_start: 0.6789 (t60) cc_final: 0.6254 (t-100) REVERT: B 231 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8153 (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: 0.9009 (p0) cc_final: 0.8464 (p0) REVERT: B 586 MET cc_start: 0.8401 (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: 0.1072 time to fit residues: 49.4120 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 : 0.534 ------------------------------------------------------------------------------- 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: 50.0000 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.102469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074388 restraints weight = 44188.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.073865 restraints weight = 37152.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074598 restraints weight = 35446.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074296 restraints weight = 26147.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075003 restraints weight = 22972.966| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1122 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= 0.158 Angle : 0.707 8.108 19730 Z= 0.342 Chirality : 0.041 0.243 2467 Planarity : 0.004 0.058 2377 Dihedral : 14.483 137.619 2752 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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 aren not related in a simple way. whole: 1.19 (0.19), residues: 1796 helix: 1.33 (0.14), residues: 1288 sheet: 0.17 (0.48), residues: 110 loop : -0.65 (0.31), residues: 398 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 0.060 0.002 TRP B 635 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00333 (14450) covalent geometry : angle 0.70732 (19730) hydrogen bonds : bond 0.05175 ( 1042) hydrogen bonds : angle 4.26602 ( 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 : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8566 (pmm) cc_final: 0.8223 (pmm) REVERT: A 199 MET cc_start: 0.8443 (ttt) cc_final: 0.7980 (ttt) REVERT: A 240 CYS cc_start: 0.8823 (m) cc_final: 0.8375 (m) REVERT: A 268 PHE cc_start: 0.8544 (t80) cc_final: 0.8161 (t80) REVERT: A 366 MET cc_start: 0.7790 (ttm) cc_final: 0.7508 (ttm) REVERT: A 401 MET cc_start: 0.9028 (ptm) cc_final: 0.8723 (ptm) REVERT: A 524 ASP cc_start: 0.9111 (p0) cc_final: 0.8412 (p0) REVERT: A 586 MET cc_start: 0.8456 (ptp) cc_final: 0.8044 (ptp) REVERT: A 590 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8403 (mt-10) REVERT: A 643 TRP cc_start: 0.6826 (t60) cc_final: 0.6403 (t-100) REVERT: A 853 ILE cc_start: 0.9149 (tp) cc_final: 0.8874 (tp) REVERT: B 160 MET cc_start: 0.8082 (ptm) cc_final: 0.7768 (ptt) REVERT: B 233 GLU cc_start: 0.8353 (tp30) cc_final: 0.8068 (tp30) REVERT: B 240 CYS cc_start: 0.8740 (m) cc_final: 0.8309 (m) REVERT: B 268 PHE cc_start: 0.8596 (t80) cc_final: 0.8194 (t80) REVERT: B 524 ASP cc_start: 0.9200 (p0) cc_final: 0.8616 (p0) REVERT: B 578 MET cc_start: 0.8453 (ppp) cc_final: 0.8244 (ppp) REVERT: B 586 MET cc_start: 0.8432 (ptp) cc_final: 0.8079 (ptp) REVERT: B 588 LYS cc_start: 0.9414 (ptpp) cc_final: 0.9190 (pttm) REVERT: B 597 GLN cc_start: 0.8754 (mp10) cc_final: 0.8477 (mp10) REVERT: B 942 MET cc_start: 0.8681 (mmm) cc_final: 0.8432 (mmm) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.0978 time to fit residues: 45.7146 Evaluate side-chains 228 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 7.9990 chunk 75 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.103215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074939 restraints weight = 44248.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.074529 restraints weight = 32183.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075085 restraints weight = 28848.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075369 restraints weight = 20666.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075582 restraints weight = 19198.255| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1462 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= 0.131 Angle : 0.658 7.936 19730 Z= 0.318 Chirality : 0.040 0.236 2467 Planarity : 0.004 0.047 2377 Dihedral : 12.179 137.147 2752 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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 aren not related in a simple way. whole: 1.38 (0.20), residues: 1796 helix: 1.47 (0.14), residues: 1290 sheet: 0.18 (0.47), residues: 110 loop : -0.56 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 875 TYR 0.025 0.001 TYR A 309 PHE 0.019 0.001 PHE B 248 TRP 0.066 0.002 TRP B 635 HIS 0.014 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00271 (14450) covalent geometry : angle 0.65821 (19730) hydrogen bonds : bond 0.04684 ( 1042) hydrogen bonds : angle 4.05592 ( 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 300 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.531 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: 0.8409 (ttt) cc_final: 0.7942 (ttt) REVERT: A 233 GLU cc_start: 0.8417 (tp30) cc_final: 0.8104 (tp30) REVERT: A 235 LEU cc_start: 0.9362 (tp) cc_final: 0.9155 (tp) REVERT: A 240 CYS cc_start: 0.8772 (m) cc_final: 0.8373 (m) REVERT: A 366 MET cc_start: 0.7739 (ttm) cc_final: 0.7349 (ttm) REVERT: A 401 MET cc_start: 0.8965 (ptm) cc_final: 0.8662 (ptm) REVERT: A 524 ASP cc_start: 0.9129 (p0) cc_final: 0.8412 (p0) REVERT: A 586 MET cc_start: 0.8423 (ptp) cc_final: 0.8053 (ptp) REVERT: A 590 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8354 (mt-10) REVERT: A 597 GLN cc_start: 0.8658 (mp10) cc_final: 0.8364 (mp10) REVERT: A 643 TRP cc_start: 0.6838 (t60) cc_final: 0.6393 (t-100) REVERT: A 853 ILE cc_start: 0.9142 (tp) cc_final: 0.8871 (tp) REVERT: B 160 MET cc_start: 0.8190 (ptm) cc_final: 0.7874 (ptt) REVERT: B 233 GLU cc_start: 0.8550 (tp30) cc_final: 0.8192 (tp30) REVERT: B 240 CYS cc_start: 0.8731 (m) cc_final: 0.8298 (m) REVERT: B 268 PHE cc_start: 0.8609 (t80) cc_final: 0.8247 (t80) REVERT: B 524 ASP cc_start: 0.9131 (p0) cc_final: 0.8417 (p0) REVERT: B 578 MET cc_start: 0.8501 (ppp) cc_final: 0.8285 (ppp) REVERT: B 586 MET cc_start: 0.8449 (ptp) cc_final: 0.8079 (ptp) REVERT: B 853 ILE cc_start: 0.9262 (tp) cc_final: 0.8960 (tp) REVERT: B 912 THR cc_start: 0.9180 (t) cc_final: 0.8805 (t) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.0936 time to fit residues: 44.5237 Evaluate side-chains 239 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 50.0000 chunk 2 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.102251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074537 restraints weight = 44503.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074290 restraints weight = 36978.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074660 restraints weight = 34914.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075454 restraints weight = 23650.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075588 restraints weight = 21718.657| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14450 Z= 0.154 Angle : 0.677 9.240 19730 Z= 0.328 Chirality : 0.041 0.241 2467 Planarity : 0.004 0.045 2377 Dihedral : 11.432 137.250 2752 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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 aren not related in a simple way. whole: 1.43 (0.20), residues: 1796 helix: 1.51 (0.14), residues: 1294 sheet: 0.19 (0.47), residues: 110 loop : -0.61 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 875 TYR 0.028 0.001 TYR A 309 PHE 0.013 0.001 PHE A 365 TRP 0.068 0.002 TRP B 635 HIS 0.003 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00333 (14450) covalent geometry : angle 0.67745 (19730) hydrogen bonds : bond 0.04647 ( 1042) hydrogen bonds : angle 4.06669 ( 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 301 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8378 (pmm) cc_final: 0.7983 (pmm) REVERT: A 199 MET cc_start: 0.8412 (ttt) cc_final: 0.8072 (ttt) REVERT: A 233 GLU cc_start: 0.8394 (tp30) cc_final: 0.8088 (tp30) REVERT: A 240 CYS cc_start: 0.8749 (m) cc_final: 0.8350 (m) REVERT: A 366 MET cc_start: 0.7591 (ttm) cc_final: 0.7366 (ttm) REVERT: A 401 MET cc_start: 0.8936 (ptm) cc_final: 0.8622 (ptm) REVERT: A 524 ASP cc_start: 0.9134 (p0) cc_final: 0.8395 (p0) REVERT: A 586 MET cc_start: 0.8405 (ptp) cc_final: 0.8023 (ptp) REVERT: A 594 TYR cc_start: 0.9553 (m-80) cc_final: 0.9102 (m-80) REVERT: A 597 GLN cc_start: 0.8699 (mp10) cc_final: 0.8477 (mp10) REVERT: A 633 LYS cc_start: 0.9348 (pttp) cc_final: 0.8827 (mtpt) REVERT: A 643 TRP cc_start: 0.6816 (t60) cc_final: 0.6393 (t-100) REVERT: A 853 ILE cc_start: 0.9094 (tp) cc_final: 0.8824 (tp) REVERT: B 160 MET cc_start: 0.8189 (ptm) cc_final: 0.7932 (ptt) REVERT: B 233 GLU cc_start: 0.8531 (tp30) cc_final: 0.8293 (tp30) REVERT: B 240 CYS cc_start: 0.8687 (m) cc_final: 0.8269 (m) REVERT: B 268 PHE cc_start: 0.8581 (t80) cc_final: 0.8194 (t80) REVERT: B 524 ASP cc_start: 0.9140 (p0) cc_final: 0.8438 (p0) REVERT: B 578 MET cc_start: 0.8492 (ppp) cc_final: 0.8269 (ppp) REVERT: B 586 MET cc_start: 0.8404 (ptp) cc_final: 0.8151 (ptt) REVERT: B 588 LYS cc_start: 0.9392 (ptpp) cc_final: 0.9165 (pttm) REVERT: B 612 VAL cc_start: 0.9486 (m) cc_final: 0.9282 (m) REVERT: B 853 ILE cc_start: 0.9226 (tp) cc_final: 0.8918 (tp) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1016 time to fit residues: 48.0676 Evaluate side-chains 240 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 0.8980 chunk 150 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.102976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074805 restraints weight = 44239.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074219 restraints weight = 35789.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074956 restraints weight = 34468.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074877 restraints weight = 23736.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075339 restraints weight = 21306.411| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1738 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= 0.136 Angle : 0.661 8.455 19730 Z= 0.319 Chirality : 0.040 0.258 2467 Planarity : 0.004 0.042 2377 Dihedral : 10.831 136.921 2752 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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 aren not related in a simple way. whole: 1.48 (0.20), residues: 1796 helix: 1.56 (0.14), residues: 1294 sheet: 0.21 (0.47), residues: 110 loop : -0.59 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 865 TYR 0.025 0.001 TYR A 309 PHE 0.012 0.001 PHE B 95 TRP 0.052 0.002 TRP A 635 HIS 0.006 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00291 (14450) covalent geometry : angle 0.66060 (19730) hydrogen bonds : bond 0.04481 ( 1042) hydrogen bonds : angle 3.99780 ( 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 310 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.541 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: 0.8512 (ttt) cc_final: 0.8101 (ttt) REVERT: A 233 GLU cc_start: 0.8464 (tp30) cc_final: 0.8085 (tp30) REVERT: A 240 CYS cc_start: 0.8769 (m) cc_final: 0.8358 (m) REVERT: A 366 MET cc_start: 0.7619 (ttm) cc_final: 0.7388 (ttm) REVERT: A 401 MET cc_start: 0.8958 (ptm) cc_final: 0.8639 (ptm) REVERT: A 524 ASP cc_start: 0.9176 (p0) cc_final: 0.8465 (p0) REVERT: A 586 MET cc_start: 0.8394 (ptp) cc_final: 0.8090 (ptp) REVERT: A 590 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8315 (mt-10) REVERT: A 597 GLN cc_start: 0.8442 (mp10) cc_final: 0.8204 (mp10) REVERT: A 643 TRP cc_start: 0.6873 (t60) cc_final: 0.6437 (t-100) REVERT: A 853 ILE cc_start: 0.9127 (tp) cc_final: 0.8851 (tp) REVERT: A 899 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7819 (ttm-80) REVERT: B 160 MET cc_start: 0.8231 (ptm) cc_final: 0.7963 (ptt) REVERT: B 233 GLU cc_start: 0.8458 (tp30) cc_final: 0.8184 (tp30) REVERT: B 240 CYS cc_start: 0.8724 (m) cc_final: 0.8314 (m) REVERT: B 268 PHE cc_start: 0.8635 (t80) cc_final: 0.8263 (t80) REVERT: B 524 ASP cc_start: 0.9169 (p0) cc_final: 0.8490 (p0) REVERT: B 586 MET cc_start: 0.8465 (ptp) cc_final: 0.8191 (ptt) REVERT: B 588 LYS cc_start: 0.9411 (ptpp) cc_final: 0.9184 (pttm) REVERT: B 614 HIS cc_start: 0.8503 (m90) cc_final: 0.8268 (m90) REVERT: B 838 ASP cc_start: 0.8944 (t0) cc_final: 0.8731 (t0) REVERT: B 853 ILE cc_start: 0.9217 (tp) cc_final: 0.8912 (tp) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.0951 time to fit residues: 46.2230 Evaluate side-chains 251 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 0.0030 chunk 158 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074419 restraints weight = 44695.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.074725 restraints weight = 29872.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075690 restraints weight = 23119.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075525 restraints weight = 17876.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.076077 restraints weight = 17156.594| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1915 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 : 0.668 9.166 19730 Z= 0.320 Chirality : 0.041 0.292 2467 Planarity : 0.004 0.040 2377 Dihedral : 10.264 136.540 2752 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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 aren not related in a simple way. whole: 1.56 (0.20), residues: 1796 helix: 1.60 (0.14), residues: 1294 sheet: 0.19 (0.47), residues: 108 loop : -0.50 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 583 TYR 0.022 0.001 TYR A 309 PHE 0.017 0.001 PHE B 365 TRP 0.085 0.002 TRP B 635 HIS 0.004 0.000 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00247 (14450) covalent geometry : angle 0.66836 (19730) hydrogen bonds : bond 0.04282 ( 1042) hydrogen bonds : angle 3.93104 ( 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 320 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.474 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: 0.8354 (pmm) cc_final: 0.7425 (pmm) REVERT: A 199 MET cc_start: 0.8502 (ttt) cc_final: 0.8095 (ttt) REVERT: A 233 GLU cc_start: 0.8478 (tp30) cc_final: 0.8073 (tp30) REVERT: A 240 CYS cc_start: 0.8748 (m) cc_final: 0.8352 (m) REVERT: A 366 MET cc_start: 0.7647 (ttm) cc_final: 0.7368 (ttm) REVERT: A 383 MET cc_start: 0.8276 (tmm) cc_final: 0.7818 (tmm) REVERT: A 401 MET cc_start: 0.9014 (ptm) cc_final: 0.8667 (ptm) REVERT: A 524 ASP cc_start: 0.9155 (p0) cc_final: 0.8449 (p0) REVERT: A 586 MET cc_start: 0.8448 (ptp) cc_final: 0.8103 (ptp) REVERT: A 590 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8388 (mt-10) REVERT: A 614 HIS cc_start: 0.8446 (m90) cc_final: 0.8238 (m90) REVERT: A 633 LYS cc_start: 0.9367 (pttp) cc_final: 0.8904 (mtpt) REVERT: A 853 ILE cc_start: 0.9145 (tp) cc_final: 0.8851 (tp) REVERT: A 899 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7809 (ttm-80) REVERT: A 923 ASP cc_start: 0.7378 (t0) cc_final: 0.6992 (t0) REVERT: A 942 MET cc_start: 0.8615 (mmm) cc_final: 0.8389 (mmm) REVERT: B 160 MET cc_start: 0.8291 (ptm) cc_final: 0.8006 (ptt) REVERT: B 233 GLU cc_start: 0.8608 (tp30) cc_final: 0.8284 (tp30) REVERT: B 240 CYS cc_start: 0.8738 (m) cc_final: 0.8313 (m) REVERT: B 268 PHE cc_start: 0.8682 (t80) cc_final: 0.8310 (t80) REVERT: B 524 ASP cc_start: 0.9154 (p0) cc_final: 0.8484 (p0) REVERT: B 586 MET cc_start: 0.8534 (ptp) cc_final: 0.8132 (tmm) REVERT: B 588 LYS cc_start: 0.9461 (ptpp) cc_final: 0.9226 (ptpp) REVERT: B 590 GLU cc_start: 0.8624 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 594 TYR cc_start: 0.9272 (m-80) cc_final: 0.8730 (m-80) REVERT: B 853 ILE cc_start: 0.9251 (tp) cc_final: 0.8947 (tp) REVERT: B 912 THR cc_start: 0.9066 (t) cc_final: 0.8839 (t) REVERT: B 923 ASP cc_start: 0.7412 (t0) cc_final: 0.7133 (t0) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.0965 time to fit residues: 48.3407 Evaluate side-chains 258 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 3.9990 chunk 82 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.103846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.070065 restraints weight = 44566.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072425 restraints weight = 23720.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073883 restraints weight = 16180.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074773 restraints weight = 12887.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075237 restraints weight = 11237.446| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2000 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= 0.125 Angle : 0.682 9.756 19730 Z= 0.327 Chirality : 0.041 0.304 2467 Planarity : 0.004 0.052 2377 Dihedral : 9.903 136.430 2752 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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 aren not related in a simple way. whole: 1.58 (0.20), residues: 1796 helix: 1.61 (0.14), residues: 1294 sheet: 0.22 (0.48), residues: 108 loop : -0.47 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.025 0.001 TYR A 387 PHE 0.021 0.001 PHE B 406 TRP 0.063 0.002 TRP A 635 HIS 0.002 0.000 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00258 (14450) covalent geometry : angle 0.68165 (19730) hydrogen bonds : bond 0.04204 ( 1042) hydrogen bonds : angle 3.93579 ( 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 316 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.674 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: 0.8415 (pmm) cc_final: 0.8195 (pmm) REVERT: A 199 MET cc_start: 0.8466 (ttt) cc_final: 0.8206 (ttt) REVERT: A 233 GLU cc_start: 0.8500 (tp30) cc_final: 0.8064 (tp30) REVERT: A 240 CYS cc_start: 0.8762 (m) cc_final: 0.8371 (m) REVERT: A 366 MET cc_start: 0.7862 (ttm) cc_final: 0.7558 (ttm) REVERT: A 387 TYR cc_start: 0.7413 (m-80) cc_final: 0.6893 (m-80) REVERT: A 401 MET cc_start: 0.8985 (ptm) cc_final: 0.8638 (ptm) REVERT: A 524 ASP cc_start: 0.9130 (p0) cc_final: 0.8402 (p0) REVERT: A 586 MET cc_start: 0.8589 (ptp) cc_final: 0.8175 (ptp) REVERT: A 590 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8473 (mt-10) REVERT: A 843 TYR cc_start: 0.9259 (t80) cc_final: 0.8889 (t80) REVERT: A 853 ILE cc_start: 0.9036 (tp) cc_final: 0.8738 (tp) REVERT: A 899 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7859 (ttm-80) REVERT: A 912 THR cc_start: 0.8060 (m) cc_final: 0.7708 (m) REVERT: A 923 ASP cc_start: 0.7432 (t0) cc_final: 0.7170 (t0) REVERT: B 124 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7201 (mp0) REVERT: B 160 MET cc_start: 0.8306 (ptm) cc_final: 0.8015 (ptt) REVERT: B 233 GLU cc_start: 0.8576 (tp30) cc_final: 0.8212 (tp30) REVERT: B 240 CYS cc_start: 0.8811 (m) cc_final: 0.8392 (m) REVERT: B 268 PHE cc_start: 0.8581 (t80) cc_final: 0.8229 (t80) REVERT: B 524 ASP cc_start: 0.9114 (p0) cc_final: 0.8420 (p0) REVERT: B 586 MET cc_start: 0.8570 (ptp) cc_final: 0.8228 (ptt) REVERT: B 588 LYS cc_start: 0.9530 (ptpp) cc_final: 0.9288 (ptpp) REVERT: B 590 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 594 TYR cc_start: 0.9297 (m-80) cc_final: 0.8802 (m-80) REVERT: B 608 LEU cc_start: 0.9493 (tp) cc_final: 0.9280 (tt) REVERT: B 838 ASP cc_start: 0.9154 (t0) cc_final: 0.8901 (t0) REVERT: B 853 ILE cc_start: 0.9176 (tp) cc_final: 0.8862 (tp) REVERT: B 912 THR cc_start: 0.9047 (t) cc_final: 0.8662 (t) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1027 time to fit residues: 50.8291 Evaluate side-chains 258 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 0.3980 chunk 175 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.103554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073882 restraints weight = 44249.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.073191 restraints weight = 32955.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073899 restraints weight = 26916.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.074331 restraints weight = 20101.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074500 restraints weight = 19408.489| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2062 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= 0.143 Angle : 0.694 10.053 19730 Z= 0.338 Chirality : 0.042 0.298 2467 Planarity : 0.004 0.046 2377 Dihedral : 9.750 136.646 2752 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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 aren not related in a simple way. whole: 1.51 (0.20), residues: 1796 helix: 1.56 (0.14), residues: 1294 sheet: 0.20 (0.48), residues: 108 loop : -0.47 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 585 TYR 0.024 0.001 TYR A 309 PHE 0.041 0.001 PHE A 365 TRP 0.072 0.002 TRP A 635 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00307 (14450) covalent geometry : angle 0.69357 (19730) hydrogen bonds : bond 0.04318 ( 1042) hydrogen bonds : angle 3.99863 ( 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 309 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.501 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: 0.8369 (pmm) cc_final: 0.7978 (pmm) REVERT: A 199 MET cc_start: 0.8519 (ttt) cc_final: 0.8125 (ttt) REVERT: A 233 GLU cc_start: 0.8549 (tp30) cc_final: 0.8251 (tp30) REVERT: A 240 CYS cc_start: 0.8797 (m) cc_final: 0.8396 (m) REVERT: A 366 MET cc_start: 0.7897 (ttm) cc_final: 0.7603 (ttm) REVERT: A 401 MET cc_start: 0.9033 (ptm) cc_final: 0.8687 (ptm) REVERT: A 524 ASP cc_start: 0.9206 (p0) cc_final: 0.8562 (p0) REVERT: A 586 MET cc_start: 0.8507 (ptp) cc_final: 0.8130 (ptp) REVERT: A 590 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8405 (mt-10) REVERT: A 838 ASP cc_start: 0.8970 (t0) cc_final: 0.8744 (t0) REVERT: A 843 TYR cc_start: 0.9083 (t80) cc_final: 0.8766 (t80) REVERT: A 853 ILE cc_start: 0.9157 (tp) cc_final: 0.8842 (tp) REVERT: A 857 MET cc_start: 0.8899 (tpt) cc_final: 0.8185 (tmm) REVERT: A 899 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7923 (ttm170) REVERT: A 912 THR cc_start: 0.8139 (m) cc_final: 0.7778 (m) REVERT: B 160 MET cc_start: 0.8318 (ptm) cc_final: 0.8037 (ptt) REVERT: B 233 GLU cc_start: 0.8457 (tp30) cc_final: 0.8057 (tp30) REVERT: B 240 CYS cc_start: 0.8812 (m) cc_final: 0.8405 (m) REVERT: B 268 PHE cc_start: 0.8773 (t80) cc_final: 0.8429 (t80) REVERT: B 346 GLU cc_start: 0.8333 (tp30) cc_final: 0.7669 (tp30) REVERT: B 524 ASP cc_start: 0.9193 (p0) cc_final: 0.8572 (p0) REVERT: B 586 MET cc_start: 0.8574 (ptp) cc_final: 0.8211 (ptt) REVERT: B 588 LYS cc_start: 0.9484 (ptpp) cc_final: 0.9278 (pttm) REVERT: B 590 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8385 (mt-10) REVERT: B 594 TYR cc_start: 0.9306 (m-80) cc_final: 0.8812 (m-80) REVERT: B 614 HIS cc_start: 0.8382 (m90) cc_final: 0.8073 (m-70) REVERT: B 853 ILE cc_start: 0.9269 (tp) cc_final: 0.8956 (tp) REVERT: B 912 THR cc_start: 0.9129 (t) cc_final: 0.8784 (t) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1011 time to fit residues: 48.9793 Evaluate side-chains 247 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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: 2.9990 chunk 156 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 71 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074960 restraints weight = 44239.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.073599 restraints weight = 31825.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074554 restraints weight = 27568.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074953 restraints weight = 20478.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075218 restraints weight = 19627.210| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14450 Z= 0.132 Angle : 0.703 11.130 19730 Z= 0.340 Chirality : 0.042 0.301 2467 Planarity : 0.004 0.051 2377 Dihedral : 9.530 136.422 2752 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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 aren not related in a simple way. whole: 1.52 (0.20), residues: 1796 helix: 1.55 (0.14), residues: 1294 sheet: 0.24 (0.48), residues: 108 loop : -0.47 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 583 TYR 0.022 0.001 TYR A 309 PHE 0.022 0.001 PHE B 248 TRP 0.106 0.002 TRP B 635 HIS 0.003 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00281 (14450) covalent geometry : angle 0.70283 (19730) hydrogen bonds : bond 0.04247 ( 1042) hydrogen bonds : angle 4.01854 ( 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 312 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.530 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 233 GLU cc_start: 0.8535 (tp30) cc_final: 0.8241 (tp30) REVERT: A 240 CYS cc_start: 0.8738 (m) cc_final: 0.8344 (m) REVERT: A 268 PHE cc_start: 0.8663 (t80) cc_final: 0.8278 (t80) REVERT: A 366 MET cc_start: 0.7779 (ttm) cc_final: 0.7479 (ttm) REVERT: A 524 ASP cc_start: 0.9209 (p0) cc_final: 0.8574 (p0) REVERT: A 586 MET cc_start: 0.8481 (ptp) cc_final: 0.8093 (ptp) REVERT: A 590 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 843 TYR cc_start: 0.9051 (t80) cc_final: 0.8768 (t80) REVERT: A 853 ILE cc_start: 0.9176 (tp) cc_final: 0.8863 (tp) REVERT: A 857 MET cc_start: 0.9092 (tpt) cc_final: 0.8374 (tmm) REVERT: A 899 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7787 (ttm-80) REVERT: A 912 THR cc_start: 0.8105 (m) cc_final: 0.7816 (m) REVERT: B 160 MET cc_start: 0.8234 (ptm) cc_final: 0.7940 (ptt) REVERT: B 233 GLU cc_start: 0.8458 (tp30) cc_final: 0.8036 (tp30) REVERT: B 240 CYS cc_start: 0.8793 (m) cc_final: 0.8381 (m) REVERT: B 268 PHE cc_start: 0.8782 (t80) cc_final: 0.8447 (t80) REVERT: B 524 ASP cc_start: 0.9216 (p0) cc_final: 0.8598 (p0) REVERT: B 586 MET cc_start: 0.8569 (ptp) cc_final: 0.8191 (ptt) REVERT: B 588 LYS cc_start: 0.9485 (ptpp) cc_final: 0.9261 (ptpp) REVERT: B 590 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 594 TYR cc_start: 0.9256 (m-80) cc_final: 0.8985 (m-80) REVERT: B 614 HIS cc_start: 0.8299 (m90) cc_final: 0.8046 (m90) REVERT: B 838 ASP cc_start: 0.8973 (t0) cc_final: 0.8747 (t0) REVERT: B 853 ILE cc_start: 0.9283 (tp) cc_final: 0.8967 (tp) REVERT: B 912 THR cc_start: 0.9105 (t) cc_final: 0.8780 (t) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.0993 time to fit residues: 48.7578 Evaluate side-chains 257 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074874 restraints weight = 44595.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073963 restraints weight = 31086.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074682 restraints weight = 27146.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075237 restraints weight = 19756.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075479 restraints weight = 18419.272| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 0.058 14450 Z= 0.134 Angle : 0.715 10.682 19730 Z= 0.346 Chirality : 0.042 0.300 2467 Planarity : 0.004 0.052 2377 Dihedral : 9.339 136.470 2752 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 aren not related in a simple way. whole: 1.50 (0.20), residues: 1796 helix: 1.54 (0.14), residues: 1292 sheet: 0.26 (0.48), residues: 108 loop : -0.46 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 865 TYR 0.022 0.001 TYR A 309 PHE 0.033 0.001 PHE B 365 TRP 0.091 0.002 TRP B 635 HIS 0.004 0.000 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00287 (14450) covalent geometry : angle 0.71538 (19730) hydrogen bonds : bond 0.04280 ( 1042) hydrogen bonds : angle 4.01731 ( 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 312 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.548 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 124 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 133 MET cc_start: 0.8486 (pmm) cc_final: 0.8177 (pmm) REVERT: A 233 GLU cc_start: 0.8571 (tp30) cc_final: 0.8281 (tp30) REVERT: A 240 CYS cc_start: 0.8730 (m) cc_final: 0.8343 (m) REVERT: A 366 MET cc_start: 0.7921 (ttm) cc_final: 0.7683 (ttm) REVERT: A 387 TYR cc_start: 0.7468 (m-80) cc_final: 0.7085 (m-10) REVERT: A 524 ASP cc_start: 0.9203 (p0) cc_final: 0.8556 (p0) REVERT: A 586 MET cc_start: 0.8460 (ptp) cc_final: 0.8087 (ptp) REVERT: A 590 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8351 (mt-10) REVERT: A 843 TYR cc_start: 0.9135 (t80) cc_final: 0.8868 (t80) REVERT: A 853 ILE cc_start: 0.9156 (tp) cc_final: 0.8835 (tp) REVERT: A 857 MET cc_start: 0.9095 (tpt) cc_final: 0.8370 (tmm) REVERT: A 899 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.7870 (ttm170) REVERT: A 900 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 912 THR cc_start: 0.8115 (m) cc_final: 0.7812 (m) REVERT: B 124 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7587 (mt-10) REVERT: B 160 MET cc_start: 0.8295 (ptm) cc_final: 0.8005 (ptt) REVERT: B 233 GLU cc_start: 0.8415 (tp30) cc_final: 0.7992 (tp30) REVERT: B 240 CYS cc_start: 0.8797 (m) cc_final: 0.8396 (m) REVERT: B 248 PHE cc_start: 0.8545 (m-80) cc_final: 0.8148 (m-10) REVERT: B 268 PHE cc_start: 0.8742 (t80) cc_final: 0.8398 (t80) REVERT: B 483 MET cc_start: 0.8522 (pmm) cc_final: 0.8280 (pmm) REVERT: B 524 ASP cc_start: 0.9201 (p0) cc_final: 0.8569 (p0) REVERT: B 586 MET cc_start: 0.8528 (ptp) cc_final: 0.8184 (ptt) REVERT: B 588 LYS cc_start: 0.9479 (ptpp) cc_final: 0.9264 (pttm) REVERT: B 590 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 614 HIS cc_start: 0.8257 (m90) cc_final: 0.7992 (m90) REVERT: B 838 ASP cc_start: 0.8977 (t0) cc_final: 0.8742 (t0) REVERT: B 853 ILE cc_start: 0.9274 (tp) cc_final: 0.8947 (tp) REVERT: B 912 THR cc_start: 0.9110 (t) cc_final: 0.8805 (t) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1018 time to fit residues: 49.7788 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 : 0.534 ------------------------------------------------------------------------------- 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: 8.9990 chunk 163 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 149 optimal weight: 0.0050 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 177 optimal weight: 40.0000 chunk 143 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 HIS B 928 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074443 restraints weight = 45213.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073822 restraints weight = 34221.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074755 restraints weight = 26852.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074969 restraints weight = 21099.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075210 restraints weight = 20272.542| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.003 0.061 14450 Z= 0.131 Angle : 0.713 10.398 19730 Z= 0.348 Chirality : 0.042 0.302 2467 Planarity : 0.004 0.054 2377 Dihedral : 9.120 136.382 2752 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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 aren not related in a simple way. whole: 1.49 (0.20), residues: 1796 helix: 1.53 (0.14), residues: 1292 sheet: 0.28 (0.48), residues: 108 loop : -0.47 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 865 TYR 0.021 0.001 TYR A 309 PHE 0.014 0.001 PHE B 95 TRP 0.087 0.002 TRP B 635 HIS 0.003 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00279 (14450) covalent geometry : angle 0.71313 (19730) hydrogen bonds : bond 0.04243 ( 1042) hydrogen bonds : angle 4.04465 ( 3078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.69 seconds wall clock time: 37 minutes 59.96 seconds (2279.96 seconds total)